src/jalview/gui/AlignFrame.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.gui;
  22
  23 import jalview.analysis.AlignmentSorter;
  24 import jalview.analysis.AlignmentUtils;
  25 import jalview.analysis.CrossRef;
  26 import jalview.analysis.Dna;
  27 import jalview.analysis.ParseProperties;
  28 import jalview.analysis.SequenceIdMatcher;
  29 import jalview.api.AlignExportSettingI;
  30 import jalview.api.AlignViewControllerGuiI;
  31 import jalview.api.AlignViewControllerI;
  32 import jalview.api.AlignViewportI;
  33 import jalview.api.AlignmentViewPanel;
  34 import jalview.api.FeatureSettingsControllerI;
  35 import jalview.api.SplitContainerI;
  36 import jalview.api.ViewStyleI;
  37 import jalview.api.analysis.SimilarityParamsI;
  38 import jalview.bin.Cache;
  39 import jalview.bin.Jalview;
  40 import jalview.commands.CommandI;
  41 import jalview.commands.EditCommand;
  42 import jalview.commands.EditCommand.Action;
  43 import jalview.commands.OrderCommand;
  44 import jalview.commands.RemoveGapColCommand;
  45 import jalview.commands.RemoveGapsCommand;
  46 import jalview.commands.SlideSequencesCommand;
  47 import jalview.commands.TrimRegionCommand;
  48 import jalview.datamodel.AlignedCodonFrame;
  49 import jalview.datamodel.Alignment;
  50 import jalview.datamodel.AlignmentAnnotation;
  51 import jalview.datamodel.AlignmentExportData;
  52 import jalview.datamodel.AlignmentI;
  53 import jalview.datamodel.AlignmentOrder;
  54 import jalview.datamodel.AlignmentView;
  55 import jalview.datamodel.ColumnSelection;
  56 import jalview.datamodel.HiddenColumns;
  57 import jalview.datamodel.HiddenSequences;
  58 import jalview.datamodel.PDBEntry;
  59 import jalview.datamodel.SeqCigar;
  60 import jalview.datamodel.Sequence;
  61 import jalview.datamodel.SequenceGroup;
  62 import jalview.datamodel.SequenceI;
  63 import jalview.gui.ColourMenuHelper.ColourChangeListener;
  64 import jalview.gui.ViewSelectionMenu.ViewSetProvider;
  65 import jalview.io.AlignmentProperties;
  66 import jalview.io.AnnotationFile;
  67 import jalview.io.BioJsHTMLOutput;
  68 import jalview.io.DataSourceType;
  69 import jalview.io.FileFormat;
  70 import jalview.io.FileFormatI;
  71 import jalview.io.FileFormats;
  72 import jalview.io.FileLoader;
  73 import jalview.io.FileParse;
  74 import jalview.io.FormatAdapter;
  75 import jalview.io.HtmlSvgOutput;
  76 import jalview.io.IdentifyFile;
  77 import jalview.io.JPredFile;
  78 import jalview.io.JalviewFileChooser;
  79 import jalview.io.JalviewFileView;
  80 import jalview.io.JnetAnnotationMaker;
  81 import jalview.io.NewickFile;
  82 import jalview.io.ScoreMatrixFile;
  83 import jalview.io.TCoffeeScoreFile;
  84 import jalview.jbgui.GAlignFrame;
  85 import jalview.schemes.ColourSchemeI;
  86 import jalview.schemes.ColourSchemes;
  87 import jalview.schemes.ResidueColourScheme;
  88 import jalview.schemes.TCoffeeColourScheme;
  89 import jalview.util.MessageManager;
  90 import jalview.viewmodel.AlignmentViewport;
  91 import jalview.viewmodel.ViewportRanges;
  92 import jalview.ws.DBRefFetcher;
  93 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
  94 import jalview.ws.jws1.Discoverer;
  95 import jalview.ws.jws2.Jws2Discoverer;
  96 import jalview.ws.jws2.jabaws2.Jws2Instance;
  97 import jalview.ws.seqfetcher.DbSourceProxy;
  98
  99 import java.awt.BorderLayout;
 100 import java.awt.Component;
 101 import java.awt.Rectangle;
 102 import java.awt.Toolkit;
 103 import java.awt.datatransfer.Clipboard;
 104 import java.awt.datatransfer.DataFlavor;
 105 import java.awt.datatransfer.StringSelection;
 106 import java.awt.datatransfer.Transferable;
 107 import java.awt.dnd.DnDConstants;
 108 import java.awt.dnd.DropTargetDragEvent;
 109 import java.awt.dnd.DropTargetDropEvent;
 110 import java.awt.dnd.DropTargetEvent;
 111 import java.awt.dnd.DropTargetListener;
 112 import java.awt.event.ActionEvent;
 113 import java.awt.event.ActionListener;
 114 import java.awt.event.FocusAdapter;
 115 import java.awt.event.FocusEvent;
 116 import java.awt.event.ItemEvent;
 117 import java.awt.event.ItemListener;
 118 import java.awt.event.KeyAdapter;
 119 import java.awt.event.KeyEvent;
 120 import java.awt.event.MouseEvent;
 121 import java.awt.print.PageFormat;
 122 import java.awt.print.PrinterJob;
 123 import java.beans.PropertyChangeEvent;
 124 import java.io.File;
 125 import java.io.FileWriter;
 126 import java.io.PrintWriter;
 127 import java.net.URL;
 128 import java.util.ArrayList;
 129 import java.util.Arrays;
 130 import java.util.Deque;
 131 import java.util.Enumeration;
 132 import java.util.Hashtable;
 133 import java.util.List;
 134 import java.util.Vector;
 135
 136 import javax.swing.JCheckBoxMenuItem;
 137 import javax.swing.JInternalFrame;
 138 import javax.swing.JLayeredPane;
 139 import javax.swing.JMenu;
 140 import javax.swing.JMenuItem;
 141 import javax.swing.SwingUtilities;
 142
 143 /**
 144  * DOCUMENT ME!
 145  *
 146  * @author $author$
 147  * @version $Revision$
 148  */
 149 public class AlignFrame extends GAlignFrame implements DropTargetListener,
 150         IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener
 151 {
 152
 153   public static final int DEFAULT_WIDTH = 700;
 154
 155   public static final int DEFAULT_HEIGHT = 500;
 156
 157   /*
 158    * The currently displayed panel (selected tabbed view if more than one)
 159    */
 160   public AlignmentPanel alignPanel;
 161
 162   AlignViewport viewport;
 163
 164   public AlignViewControllerI avc;
 165
 166   List<AlignmentPanel> alignPanels = new ArrayList<>();
 167
 168   /**
 169    * Last format used to load or save alignments in this window
 170    */
 171   FileFormatI currentFileFormat = null;
 172
 173   /**
 174    * Current filename for this alignment
 175    */
 176   String fileName = null;
 177
 178   /**
 179    * Creates a new AlignFrame object with specific width and height.
 180    *
 181    * @param al
 182    * @param width
 183    * @param height
 184    */
 185   public AlignFrame(AlignmentI al, int width, int height)
 186   {
 187     this(al, null, width, height);
 188   }
 189
 190   /**
 191    * Creates a new AlignFrame object with specific width, height and
 192    * sequenceSetId
 193    *
 194    * @param al
 195    * @param width
 196    * @param height
 197    * @param sequenceSetId
 198    */
 199   public AlignFrame(AlignmentI al, int width, int height,
 200           String sequenceSetId)
 201   {
 202     this(al, null, width, height, sequenceSetId);
 203   }
 204
 205   /**
 206    * Creates a new AlignFrame object with specific width, height and
 207    * sequenceSetId
 208    *
 209    * @param al
 210    * @param width
 211    * @param height
 212    * @param sequenceSetId
 213    * @param viewId
 214    */
 215   public AlignFrame(AlignmentI al, int width, int height,
 216           String sequenceSetId, String viewId)
 217   {
 218     this(al, null, width, height, sequenceSetId, viewId);
 219   }
 220
 221   /**
 222    * new alignment window with hidden columns
 223    *
 224    * @param al
 225    *          AlignmentI
 226    * @param hiddenColumns
 227    *          ColumnSelection or null
 228    * @param width
 229    *          Width of alignment frame
 230    * @param height
 231    *          height of frame.
 232    */
 233   public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
 234           int height)
 235   {
 236     this(al, hiddenColumns, width, height, null);
 237   }
 238
 239   /**
 240    * Create alignment frame for al with hiddenColumns, a specific width and
 241    * height, and specific sequenceId
 242    *
 243    * @param al
 244    * @param hiddenColumns
 245    * @param width
 246    * @param height
 247    * @param sequenceSetId
 248    *          (may be null)
 249    */
 250   public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
 251           int height, String sequenceSetId)
 252   {
 253     this(al, hiddenColumns, width, height, sequenceSetId, null);
 254   }
 255
 256   /**
 257    * Create alignment frame for al with hiddenColumns, a specific width and
 258    * height, and specific sequenceId
 259    *
 260    * @param al
 261    * @param hiddenColumns
 262    * @param width
 263    * @param height
 264    * @param sequenceSetId
 265    *          (may be null)
 266    * @param viewId
 267    *          (may be null)
 268    */
 269   public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
 270           int height, String sequenceSetId, String viewId)
 271   {
 272     setSize(width, height);
 273
 274     if (al.getDataset() == null)
 275     {
 276       al.setDataset(null);
 277     }
 278
 279     viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
 280
 281     alignPanel = new AlignmentPanel(this, viewport);
 282
 283     addAlignmentPanel(alignPanel, true);
 284     init();
 285   }
 286
 287   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
 288           HiddenColumns hiddenColumns, int width, int height)
 289   {
 290     setSize(width, height);
 291
 292     if (al.getDataset() == null)
 293     {
 294       al.setDataset(null);
 295     }
 296
 297     viewport = new AlignViewport(al, hiddenColumns);
 298
 299     if (hiddenSeqs != null && hiddenSeqs.length > 0)
 300     {
 301       viewport.hideSequence(hiddenSeqs);
 302     }
 303     alignPanel = new AlignmentPanel(this, viewport);
 304     addAlignmentPanel(alignPanel, true);
 305     init();
 306   }
 307
 308   /**
 309    * Make a new AlignFrame from existing alignmentPanels
 310    *
 311    * @param ap
 312    *          AlignmentPanel
 313    * @param av
 314    *          AlignViewport
 315    */
 316   public AlignFrame(AlignmentPanel ap)
 317   {
 318     viewport = ap.av;
 319     alignPanel = ap;
 320     addAlignmentPanel(ap, false);
 321     init();
 322   }
 323
 324   /**
 325    * initalise the alignframe from the underlying viewport data and the
 326    * configurations
 327    */
 328   void init()
 329   {
 330     if (!Jalview.isHeadlessMode())
 331     {
 332       progressBar = new ProgressBar(this.statusPanel, this.statusBar);
 333     }
 334
 335     avc = new jalview.controller.AlignViewController(this, viewport,
 336             alignPanel);
 337     if (viewport.getAlignmentConservationAnnotation() == null)
 338     {
 339       // BLOSUM62Colour.setEnabled(false);
 340       conservationMenuItem.setEnabled(false);
 341       modifyConservation.setEnabled(false);
 342       // PIDColour.setEnabled(false);
 343       // abovePIDThreshold.setEnabled(false);
 344       // modifyPID.setEnabled(false);
 345     }
 346
 347     String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
 348             "No sort");
 349
 350     if (sortby.equals("Id"))
 351     {
 352       sortIDMenuItem_actionPerformed(null);
 353     }
 354     else if (sortby.equals("Pairwise Identity"))
 355     {
 356       sortPairwiseMenuItem_actionPerformed(null);
 357     }
 358
 359     this.alignPanel.av
 360             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
 361
 362     setMenusFromViewport(viewport);
 363     buildSortByAnnotationScoresMenu();
 364     calculateTree.addActionListener(new ActionListener()
 365     {
 366
 367       @Override
 368       public void actionPerformed(ActionEvent e)
 369       {
 370         openTreePcaDialog();
 371       }
 372     });
 373     buildColourMenu();
 374
 375     if (Desktop.desktop != null)
 376     {
 377       this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
 378       addServiceListeners();
 379       setGUINucleotide();
 380     }
 381
 382     if (viewport.getWrapAlignment())
 383     {
 384       wrapMenuItem_actionPerformed(null);
 385     }
 386
 387     if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
 388     {
 389       this.overviewMenuItem_actionPerformed(null);
 390     }
 391
 392     addKeyListener();
 393
 394     final List<AlignmentPanel> selviews = new ArrayList<>();
 395     final List<AlignmentPanel> origview = new ArrayList<>();
 396     final String menuLabel = MessageManager
 397             .getString("label.copy_format_from");
 398     ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
 399             new ViewSetProvider()
 400             {
 401
 402               @Override
 403               public AlignmentPanel[] getAllAlignmentPanels()
 404               {
 405                 origview.clear();
 406                 origview.add(alignPanel);
 407                 // make an array of all alignment panels except for this one
 408                 List<AlignmentPanel> aps = new ArrayList<>(
 409                         Arrays.asList(Desktop.getAlignmentPanels(null)));
 410                 aps.remove(AlignFrame.this.alignPanel);
 411                 return aps.toArray(new AlignmentPanel[aps.size()]);
 412               }
 413             }, selviews, new ItemListener()
 414             {
 415
 416               @Override
 417               public void itemStateChanged(ItemEvent e)
 418               {
 419                 if (origview.size() > 0)
 420                 {
 421                   final AlignmentPanel ap = origview.get(0);
 422
 423                   /*
 424                    * Copy the ViewStyle of the selected panel to 'this one'.
 425                    * Don't change value of 'scaleProteinAsCdna' unless copying
 426                    * from a SplitFrame.
 427                    */
 428                   ViewStyleI vs = selviews.get(0).getAlignViewport()
 429                           .getViewStyle();
 430                   boolean fromSplitFrame = selviews.get(0)
 431                           .getAlignViewport().getCodingComplement() != null;
 432                   if (!fromSplitFrame)
 433                   {
 434                     vs.setScaleProteinAsCdna(ap.getAlignViewport()
 435                             .getViewStyle().isScaleProteinAsCdna());
 436                   }
 437                   ap.getAlignViewport().setViewStyle(vs);
 438
 439                   /*
 440                    * Also rescale ViewStyle of SplitFrame complement if there is
 441                    * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
 442                    * the whole ViewStyle (allow cDNA protein to have different
 443                    * fonts)
 444                    */
 445                   AlignViewportI complement = ap.getAlignViewport()
 446                           .getCodingComplement();
 447                   if (complement != null && vs.isScaleProteinAsCdna())
 448                   {
 449                     AlignFrame af = Desktop.getAlignFrameFor(complement);
 450                     ((SplitFrame) af.getSplitViewContainer())
 451                             .adjustLayout();
 452                     af.setMenusForViewport();
 453                   }
 454
 455                   ap.updateLayout();
 456                   ap.setSelected(true);
 457                   ap.alignFrame.setMenusForViewport();
 458
 459                 }
 460               }
 461             });
 462     if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
 463             .indexOf("devel") > -1
 464             || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
 465                     .indexOf("test") > -1)
 466     {
 467       formatMenu.add(vsel);
 468     }
 469     addFocusListener(new FocusAdapter()
 470     {
 471       @Override
 472       public void focusGained(FocusEvent e)
 473       {
 474         Jalview.setCurrentAlignFrame(AlignFrame.this);
 475       }
 476     });
 477
 478   }
 479
 480   /**
 481    * Change the filename and format for the alignment, and enable the 'reload'
 482    * button functionality.
 483    *
 484    * @param file
 485    *          valid filename
 486    * @param format
 487    *          format of file
 488    */
 489   public void setFileName(String file, FileFormatI format)
 490   {
 491     fileName = file;
 492     setFileFormat(format);
 493     reload.setEnabled(true);
 494   }
 495
 496   /**
 497    * Add a KeyListener with handlers for various KeyPressed and KeyReleased
 498    * events
 499    */
 500   void addKeyListener()
 501   {
 502     addKeyListener(new KeyAdapter()
 503     {
 504       @Override
 505       public void keyPressed(KeyEvent evt)
 506       {
 507         if (viewport.cursorMode
 508                 && ((evt.getKeyCode() >= KeyEvent.VK_0
 509                         && evt.getKeyCode() <= KeyEvent.VK_9)
 510                         || (evt.getKeyCode() >= KeyEvent.VK_NUMPAD0
 511                                 && evt.getKeyCode() <= KeyEvent.VK_NUMPAD9))
 512                 && Character.isDigit(evt.getKeyChar()))
 513         {
 514           alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
 515         }
 516
 517         switch (evt.getKeyCode())
 518         {
 519
 520         case 27: // escape key
 521           deselectAllSequenceMenuItem_actionPerformed(null);
 522
 523           break;
 524
 525         case KeyEvent.VK_DOWN:
 526           if (evt.isAltDown() || !viewport.cursorMode)
 527           {
 528             moveSelectedSequences(false);
 529           }
 530           if (viewport.cursorMode)
 531           {
 532             alignPanel.getSeqPanel().moveCursor(0, 1);
 533           }
 534           break;
 535
 536         case KeyEvent.VK_UP:
 537           if (evt.isAltDown() || !viewport.cursorMode)
 538           {
 539             moveSelectedSequences(true);
 540           }
 541           if (viewport.cursorMode)
 542           {
 543             alignPanel.getSeqPanel().moveCursor(0, -1);
 544           }
 545
 546           break;
 547
 548         case KeyEvent.VK_LEFT:
 549           if (evt.isAltDown() || !viewport.cursorMode)
 550           {
 551             slideSequences(false,
 552                     alignPanel.getSeqPanel().getKeyboardNo1());
 553           }
 554           else
 555           {
 556             alignPanel.getSeqPanel().moveCursor(-1, 0);
 557           }
 558
 559           break;
 560
 561         case KeyEvent.VK_RIGHT:
 562           if (evt.isAltDown() || !viewport.cursorMode)
 563           {
 564             slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
 565           }
 566           else
 567           {
 568             alignPanel.getSeqPanel().moveCursor(1, 0);
 569           }
 570           break;
 571
 572         case KeyEvent.VK_SPACE:
 573           if (viewport.cursorMode)
 574           {
 575             alignPanel.getSeqPanel().insertGapAtCursor(evt.isControlDown()
 576                     || evt.isShiftDown() || evt.isAltDown());
 577           }
 578           break;
 579
 580         // case KeyEvent.VK_A:
 581         // if (viewport.cursorMode)
 582         // {
 583         // alignPanel.seqPanel.insertNucAtCursor(false,"A");
 584         // //System.out.println("A");
 585         // }
 586         // break;
 587         /*
 588          * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
 589          * System.out.println("closing bracket"); } break;
 590          */
 591         case KeyEvent.VK_DELETE:
 592         case KeyEvent.VK_BACK_SPACE:
 593           if (!viewport.cursorMode)
 594           {
 595             cut_actionPerformed(null);
 596           }
 597           else
 598           {
 599             alignPanel.getSeqPanel().deleteGapAtCursor(evt.isControlDown()
 600                     || evt.isShiftDown() || evt.isAltDown());
 601           }
 602
 603           break;
 604
 605         case KeyEvent.VK_S:
 606           if (viewport.cursorMode)
 607           {
 608             alignPanel.getSeqPanel().setCursorRow();
 609           }
 610           break;
 611         case KeyEvent.VK_C:
 612           if (viewport.cursorMode && !evt.isControlDown())
 613           {
 614             alignPanel.getSeqPanel().setCursorColumn();
 615           }
 616           break;
 617         case KeyEvent.VK_P:
 618           if (viewport.cursorMode)
 619           {
 620             alignPanel.getSeqPanel().setCursorPosition();
 621           }
 622           break;
 623
 624         case KeyEvent.VK_ENTER:
 625         case KeyEvent.VK_COMMA:
 626           if (viewport.cursorMode)
 627           {
 628             alignPanel.getSeqPanel().setCursorRowAndColumn();
 629           }
 630           break;
 631
 632         case KeyEvent.VK_Q:
 633           if (viewport.cursorMode)
 634           {
 635             alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
 636           }
 637           break;
 638         case KeyEvent.VK_M:
 639           if (viewport.cursorMode)
 640           {
 641             alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
 642           }
 643           break;
 644
 645         case KeyEvent.VK_F2:
 646           viewport.cursorMode = !viewport.cursorMode;
 647           statusBar.setText(MessageManager
 648                   .formatMessage("label.keyboard_editing_mode", new String[]
 649                   { (viewport.cursorMode ? "on" : "off") }));
 650           if (viewport.cursorMode)
 651           {
 652             ViewportRanges ranges = viewport.getRanges();
 653             alignPanel.getSeqPanel().seqCanvas.cursorX = ranges
 654                     .getStartRes();
 655             alignPanel.getSeqPanel().seqCanvas.cursorY = ranges
 656                     .getStartSeq();
 657           }
 658           alignPanel.getSeqPanel().seqCanvas.repaint();
 659           break;
 660
 661         case KeyEvent.VK_F1:
 662           try
 663           {
 664             Help.showHelpWindow();
 665           } catch (Exception ex)
 666           {
 667             ex.printStackTrace();
 668           }
 669           break;
 670         case KeyEvent.VK_H:
 671         {
 672           boolean toggleSeqs = !evt.isControlDown();
 673           boolean toggleCols = !evt.isShiftDown();
 674           toggleHiddenRegions(toggleSeqs, toggleCols);
 675           break;
 676         }
 677         case KeyEvent.VK_B:
 678         {
 679           boolean toggleSel = evt.isControlDown() || evt.isMetaDown();
 680           boolean modifyExisting = true; // always modify, don't clear
 681                                          // evt.isShiftDown();
 682           boolean invertHighlighted = evt.isAltDown();
 683           avc.markHighlightedColumns(invertHighlighted, modifyExisting,
 684                   toggleSel);
 685           break;
 686         }
 687         case KeyEvent.VK_PAGE_UP:
 688           viewport.getRanges().pageUp();
 689           break;
 690         case KeyEvent.VK_PAGE_DOWN:
 691           viewport.getRanges().pageDown();
 692           break;
 693         }
 694       }
 695
 696       @Override
 697       public void keyReleased(KeyEvent evt)
 698       {
 699         switch (evt.getKeyCode())
 700         {
 701         case KeyEvent.VK_LEFT:
 702           if (evt.isAltDown() || !viewport.cursorMode)
 703           {
 704             viewport.firePropertyChange("alignment", null,
 705                     viewport.getAlignment().getSequences());
 706           }
 707           break;
 708
 709         case KeyEvent.VK_RIGHT:
 710           if (evt.isAltDown() || !viewport.cursorMode)
 711           {
 712             viewport.firePropertyChange("alignment", null,
 713                     viewport.getAlignment().getSequences());
 714           }
 715           break;
 716         }
 717       }
 718     });
 719   }
 720
 721   public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
 722   {
 723     ap.alignFrame = this;
 724     avc = new jalview.controller.AlignViewController(this, viewport,
 725             alignPanel);
 726
 727     alignPanels.add(ap);
 728
 729     PaintRefresher.Register(ap, ap.av.getSequenceSetId());
 730
 731     int aSize = alignPanels.size();
 732
 733     tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
 734
 735     if (aSize == 1 && ap.av.viewName == null)
 736     {
 737       this.getContentPane().add(ap, BorderLayout.CENTER);
 738     }
 739     else
 740     {
 741       if (aSize == 2)
 742       {
 743         setInitialTabVisible();
 744       }
 745
 746       expandViews.setEnabled(true);
 747       gatherViews.setEnabled(true);
 748       tabbedPane.addTab(ap.av.viewName, ap);
 749
 750       ap.setVisible(false);
 751     }
 752
 753     if (newPanel)
 754     {
 755       if (ap.av.isPadGaps())
 756       {
 757         ap.av.getAlignment().padGaps();
 758       }
 759       ap.av.updateConservation(ap);
 760       ap.av.updateConsensus(ap);
 761       ap.av.updateStrucConsensus(ap);
 762     }
 763   }
 764
 765   public void setInitialTabVisible()
 766   {
 767     expandViews.setEnabled(true);
 768     gatherViews.setEnabled(true);
 769     tabbedPane.setVisible(true);
 770     AlignmentPanel first = alignPanels.get(0);
 771     tabbedPane.addTab(first.av.viewName, first);
 772     this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
 773   }
 774
 775   public AlignViewport getViewport()
 776   {
 777     return viewport;
 778   }
 779
 780   /* Set up intrinsic listeners for dynamically generated GUI bits. */
 781   private void addServiceListeners()
 782   {
 783     final java.beans.PropertyChangeListener thisListener;
 784     Desktop.instance.addJalviewPropertyChangeListener("services",
 785             thisListener = new java.beans.PropertyChangeListener()
 786             {
 787               @Override
 788               public void propertyChange(PropertyChangeEvent evt)
 789               {
 790                 // // System.out.println("Discoverer property change.");
 791                 // if (evt.getPropertyName().equals("services"))
 792                 {
 793                   SwingUtilities.invokeLater(new Runnable()
 794                   {
 795
 796                     @Override
 797                     public void run()
 798                     {
 799                       System.err.println(
 800                               "Rebuild WS Menu for service change");
 801                       BuildWebServiceMenu();
 802                     }
 803
 804                   });
 805                 }
 806               }
 807             });
 808     addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
 809     {
 810       @Override
 811       public void internalFrameClosed(
 812               javax.swing.event.InternalFrameEvent evt)
 813       {
 814         // System.out.println("deregistering discoverer listener");
 815         Desktop.instance.removeJalviewPropertyChangeListener("services",
 816                 thisListener);
 817         closeMenuItem_actionPerformed(true);
 818       };
 819     });
 820     // Finally, build the menu once to get current service state
 821     new Thread(new Runnable()
 822     {
 823       @Override
 824       public void run()
 825       {
 826         BuildWebServiceMenu();
 827       }
 828     }).start();
 829   }
 830
 831   /**
 832    * Configure menu items that vary according to whether the alignment is
 833    * nucleotide or protein
 834    */
 835   public void setGUINucleotide()
 836   {
 837     AlignmentI al = getViewport().getAlignment();
 838     boolean nucleotide = al.isNucleotide();
 839
 840     showTranslation.setVisible(nucleotide);
 841     showReverse.setVisible(nucleotide);
 842     showReverseComplement.setVisible(nucleotide);
 843     conservationMenuItem.setEnabled(!nucleotide);
 844     modifyConservation
 845             .setEnabled(!nucleotide && conservationMenuItem.isSelected());
 846     showGroupConservation.setEnabled(!nucleotide);
 847
 848     showComplementMenuItem
 849             .setText(nucleotide ? MessageManager.getString("label.protein")
 850                     : MessageManager.getString("label.nucleotide"));
 851   }
 852
 853   /**
 854    * set up menus for the current viewport. This may be called after any
 855    * operation that affects the data in the current view (selection changed,
 856    * etc) to update the menus to reflect the new state.
 857    */
 858   @Override
 859   public void setMenusForViewport()
 860   {
 861     setMenusFromViewport(viewport);
 862   }
 863
 864   /**
 865    * Need to call this method when tabs are selected for multiple views, or when
 866    * loading from Jalview2XML.java
 867    *
 868    * @param av
 869    *          AlignViewport
 870    */
 871   void setMenusFromViewport(AlignViewport av)
 872   {
 873     padGapsMenuitem.setSelected(av.isPadGaps());
 874     colourTextMenuItem.setSelected(av.isShowColourText());
 875     abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
 876     modifyPID.setEnabled(abovePIDThreshold.isSelected());
 877     conservationMenuItem.setSelected(av.getConservationSelected());
 878     modifyConservation.setEnabled(conservationMenuItem.isSelected());
 879     seqLimits.setSelected(av.getShowJVSuffix());
 880     idRightAlign.setSelected(av.isRightAlignIds());
 881     centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
 882     renderGapsMenuItem.setSelected(av.isRenderGaps());
 883     wrapMenuItem.setSelected(av.getWrapAlignment());
 884     scaleAbove.setVisible(av.getWrapAlignment());
 885     scaleLeft.setVisible(av.getWrapAlignment());
 886     scaleRight.setVisible(av.getWrapAlignment());
 887     annotationPanelMenuItem.setState(av.isShowAnnotation());
 888     /*
 889      * Show/hide annotations only enabled if annotation panel is shown
 890      */
 891     showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 892     hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 893     showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 894     hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 895     viewBoxesMenuItem.setSelected(av.getShowBoxes());
 896     viewTextMenuItem.setSelected(av.getShowText());
 897     showNonconservedMenuItem.setSelected(av.getShowUnconserved());
 898     showGroupConsensus.setSelected(av.isShowGroupConsensus());
 899     showGroupConservation.setSelected(av.isShowGroupConservation());
 900     showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
 901     showSequenceLogo.setSelected(av.isShowSequenceLogo());
 902     normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
 903
 904     ColourMenuHelper.setColourSelected(colourMenu,
 905             av.getGlobalColourScheme());
 906
 907     showSeqFeatures.setSelected(av.isShowSequenceFeatures());
 908     hiddenMarkers.setState(av.getShowHiddenMarkers());
 909     applyToAllGroups.setState(av.getColourAppliesToAllGroups());
 910     showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
 911     showDbRefsMenuitem.setSelected(av.isShowDBRefs());
 912     autoCalculate.setSelected(av.autoCalculateConsensus);
 913     sortByTree.setSelected(av.sortByTree);
 914     listenToViewSelections.setSelected(av.followSelection);
 915
 916     showProducts.setEnabled(canShowProducts());
 917     setGroovyEnabled(Desktop.getGroovyConsole() != null);
 918
 919     updateEditMenuBar();
 920   }
 921
 922   /**
 923    * Set the enabled state of the 'Run Groovy' option in the Calculate menu
 924    *
 925    * @param b
 926    */
 927   public void setGroovyEnabled(boolean b)
 928   {
 929     runGroovy.setEnabled(b);
 930   }
 931
 932   private IProgressIndicator progressBar;
 933
 934   /*
 935    * (non-Javadoc)
 936    *
 937    * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
 938    */
 939   @Override
 940   public void setProgressBar(String message, long id)
 941   {
 942     progressBar.setProgressBar(message, id);
 943   }
 944
 945   @Override
 946   public void registerHandler(final long id,
 947           final IProgressIndicatorHandler handler)
 948   {
 949     progressBar.registerHandler(id, handler);
 950   }
 951
 952   /**
 953    *
 954    * @return true if any progress bars are still active
 955    */
 956   @Override
 957   public boolean operationInProgress()
 958   {
 959     return progressBar.operationInProgress();
 960   }
 961
 962   @Override
 963   public void setStatus(String text)
 964   {
 965     statusBar.setText(text);
 966   }
 967
 968   /*
 969    * Added so Castor Mapping file can obtain Jalview Version
 970    */
 971   public String getVersion()
 972   {
 973     return jalview.bin.Cache.getProperty("VERSION");
 974   }
 975
 976   public FeatureRenderer getFeatureRenderer()
 977   {
 978     return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
 979   }
 980
 981   @Override
 982   public void fetchSequence_actionPerformed(ActionEvent e)
 983   {
 984     new jalview.gui.SequenceFetcher(this);
 985   }
 986
 987   @Override
 988   public void addFromFile_actionPerformed(ActionEvent e)
 989   {
 990     Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
 991   }
 992
 993   @Override
 994   public void reload_actionPerformed(ActionEvent e)
 995   {
 996     if (fileName != null)
 997     {
 998       // TODO: JAL-1108 - ensure all associated frames are closed regardless of
 999       // originating file's format
1000       // TODO: work out how to recover feature settings for correct view(s) when
1001       // file is reloaded.
1002       if (FileFormat.Jalview.equals(currentFileFormat))
1003       {
1004         JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1005         for (int i = 0; i < frames.length; i++)
1006         {
1007           if (frames[i] instanceof AlignFrame && frames[i] != this
1008                   && ((AlignFrame) frames[i]).fileName != null
1009                   && ((AlignFrame) frames[i]).fileName.equals(fileName))
1010           {
1011             try
1012             {
1013               frames[i].setSelected(true);
1014               Desktop.instance.closeAssociatedWindows();
1015             } catch (java.beans.PropertyVetoException ex)
1016             {
1017             }
1018           }
1019
1020         }
1021         Desktop.instance.closeAssociatedWindows();
1022
1023         FileLoader loader = new FileLoader();
1024         DataSourceType protocol = fileName.startsWith("http:")
1025                 ? DataSourceType.URL
1026                 : DataSourceType.FILE;
1027         loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1028       }
1029       else
1030       {
1031         Rectangle bounds = this.getBounds();
1032
1033         FileLoader loader = new FileLoader();
1034         DataSourceType protocol = fileName.startsWith("http:")
1035                 ? DataSourceType.URL
1036                 : DataSourceType.FILE;
1037         AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
1038                 protocol, currentFileFormat);
1039
1040         newframe.setBounds(bounds);
1041         if (featureSettings != null && featureSettings.isShowing())
1042         {
1043           final Rectangle fspos = featureSettings.frame.getBounds();
1044           // TODO: need a 'show feature settings' function that takes bounds -
1045           // need to refactor Desktop.addFrame
1046           newframe.featureSettings_actionPerformed(null);
1047           final FeatureSettings nfs = newframe.featureSettings;
1048           SwingUtilities.invokeLater(new Runnable()
1049           {
1050             @Override
1051             public void run()
1052             {
1053               nfs.frame.setBounds(fspos);
1054             }
1055           });
1056           this.featureSettings.close();
1057           this.featureSettings = null;
1058         }
1059         this.closeMenuItem_actionPerformed(true);
1060       }
1061     }
1062   }
1063
1064   @Override
1065   public void addFromText_actionPerformed(ActionEvent e)
1066   {
1067     Desktop.instance
1068             .inputTextboxMenuItem_actionPerformed(viewport.getAlignPanel());
1069   }
1070
1071   @Override
1072   public void addFromURL_actionPerformed(ActionEvent e)
1073   {
1074     Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1075   }
1076
1077   @Override
1078   public void save_actionPerformed(ActionEvent e)
1079   {
1080     if (fileName == null || (currentFileFormat == null)
1081             || fileName.startsWith("http"))
1082     {
1083       saveAs_actionPerformed(null);
1084     }
1085     else
1086     {
1087       saveAlignment(fileName, currentFileFormat);
1088     }
1089   }
1090
1091   /**
1092    * DOCUMENT ME!
1093    *
1094    * @param e
1095    *          DOCUMENT ME!
1096    */
1097   @Override
1098   public void saveAs_actionPerformed(ActionEvent e)
1099   {
1100     String format = currentFileFormat == null ? null
1101             : currentFileFormat.getName();
1102     JalviewFileChooser chooser = JalviewFileChooser
1103             .forWrite(Cache.getProperty("LAST_DIRECTORY"), format);
1104
1105     chooser.setFileView(new JalviewFileView());
1106     chooser.setDialogTitle(
1107             MessageManager.getString("label.save_alignment_to_file"));
1108     chooser.setToolTipText(MessageManager.getString("action.save"));
1109
1110     int value = chooser.showSaveDialog(this);
1111
1112     if (value == JalviewFileChooser.APPROVE_OPTION)
1113     {
1114       currentFileFormat = chooser.getSelectedFormat();
1115       while (currentFileFormat == null)
1116       {
1117         JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1118                 MessageManager.getString(
1119                         "label.select_file_format_before_saving"),
1120                 MessageManager.getString("label.file_format_not_specified"),
1121                 JvOptionPane.WARNING_MESSAGE);
1122         currentFileFormat = chooser.getSelectedFormat();
1123         value = chooser.showSaveDialog(this);
1124         if (value != JalviewFileChooser.APPROVE_OPTION)
1125         {
1126           return;
1127         }
1128       }
1129
1130       fileName = chooser.getSelectedFile().getPath();
1131
1132       Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat.getName());
1133
1134       Cache.setProperty("LAST_DIRECTORY", fileName);
1135       saveAlignment(fileName, currentFileFormat);
1136     }
1137   }
1138
1139   public boolean saveAlignment(String file, FileFormatI format)
1140   {
1141     boolean success = true;
1142
1143     if (FileFormat.Jalview.equals(format))
1144     {
1145       String shortName = title;
1146
1147       if (shortName.indexOf(java.io.File.separatorChar) > -1)
1148       {
1149         shortName = shortName.substring(
1150                 shortName.lastIndexOf(java.io.File.separatorChar) + 1);
1151       }
1152
1153       success = new Jalview2XML().saveAlignment(this, file, shortName);
1154
1155       statusBar.setText(MessageManager.formatMessage(
1156               "label.successfully_saved_to_file_in_format", new Object[]
1157               { fileName, format }));
1158
1159     }
1160     else
1161     {
1162       AlignmentExportData exportData = getAlignmentForExport(format,
1163               viewport, null);
1164       if (exportData.getSettings().isCancelled())
1165       {
1166         return false;
1167       }
1168       FormatAdapter f = new FormatAdapter(alignPanel,
1169               exportData.getSettings());
1170       String output = f.formatSequences(format, exportData.getAlignment(), // class
1171                                                                            // cast
1172                                                                            // exceptions
1173                                                                            // will
1174               // occur in the distant future
1175               exportData.getOmitHidden(), exportData.getStartEndPostions(),
1176               f.getCacheSuffixDefault(format),
1177               viewport.getAlignment().getHiddenColumns());
1178
1179       if (output == null)
1180       {
1181         success = false;
1182       }
1183       else
1184       {
1185         try
1186         {
1187           PrintWriter out = new PrintWriter(new FileWriter(file));
1188
1189           out.print(output);
1190           out.close();
1191           this.setTitle(file);
1192           statusBar.setText(MessageManager.formatMessage(
1193                   "label.successfully_saved_to_file_in_format", new Object[]
1194                   { fileName, format.getName() }));
1195         } catch (Exception ex)
1196         {
1197           success = false;
1198           ex.printStackTrace();
1199         }
1200       }
1201     }
1202
1203     if (!success)
1204     {
1205       JvOptionPane.showInternalMessageDialog(this, MessageManager
1206               .formatMessage("label.couldnt_save_file", new Object[]
1207               { fileName }),
1208               MessageManager.getString("label.error_saving_file"),
1209               JvOptionPane.WARNING_MESSAGE);
1210     }
1211
1212     return success;
1213   }
1214
1215   private void warningMessage(String warning, String title)
1216   {
1217     if (new jalview.util.Platform().isHeadless())
1218     {
1219       System.err.println("Warning: " + title + "\nWarning: " + warning);
1220
1221     }
1222     else
1223     {
1224       JvOptionPane.showInternalMessageDialog(this, warning, title,
1225               JvOptionPane.WARNING_MESSAGE);
1226     }
1227     return;
1228   }
1229
1230   /**
1231    * DOCUMENT ME!
1232    *
1233    * @param e
1234    *          DOCUMENT ME!
1235    */
1236   @Override
1237   protected void outputText_actionPerformed(ActionEvent e)
1238   {
1239     FileFormatI fileFormat = FileFormats.getInstance()
1240             .forName(e.getActionCommand());
1241     AlignmentExportData exportData = getAlignmentForExport(fileFormat,
1242             viewport, null);
1243     if (exportData.getSettings().isCancelled())
1244     {
1245       return;
1246     }
1247     CutAndPasteTransfer cap = new CutAndPasteTransfer();
1248     cap.setForInput(null);
1249     try
1250     {
1251       FileFormatI format = fileFormat;
1252       cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
1253               .formatSequences(format, exportData.getAlignment(),
1254                       exportData.getOmitHidden(),
1255                       exportData.getStartEndPostions(),
1256                       viewport.getAlignment().getHiddenColumns()));
1257       Desktop.addInternalFrame(cap, MessageManager
1258               .formatMessage("label.alignment_output_command", new Object[]
1259               { e.getActionCommand() }), 600, 500);
1260     } catch (OutOfMemoryError oom)
1261     {
1262       new OOMWarning("Outputting alignment as " + e.getActionCommand(),
1263               oom);
1264       cap.dispose();
1265     }
1266
1267   }
1268
1269   public static AlignmentExportData getAlignmentForExport(
1270           FileFormatI format, AlignViewportI viewport,
1271           AlignExportSettingI exportSettings)
1272   {
1273     AlignmentI alignmentToExport = null;
1274     AlignExportSettingI settings = exportSettings;
1275     String[] omitHidden = null;
1276
1277     HiddenSequences hiddenSeqs = viewport.getAlignment()
1278             .getHiddenSequences();
1279
1280     alignmentToExport = viewport.getAlignment();
1281
1282     boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
1283     if (settings == null)
1284     {
1285       settings = new AlignExportSettings(hasHiddenSeqs,
1286               viewport.hasHiddenColumns(), format);
1287     }
1288     // settings.isExportAnnotations();
1289
1290     if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
1291     {
1292       omitHidden = viewport.getViewAsString(false,
1293               settings.isExportHiddenSequences());
1294     }
1295
1296     int[] alignmentStartEnd = new int[2];
1297     if (hasHiddenSeqs && settings.isExportHiddenSequences())
1298     {
1299       alignmentToExport = hiddenSeqs.getFullAlignment();
1300     }
1301     else
1302     {
1303       alignmentToExport = viewport.getAlignment();
1304     }
1305     alignmentStartEnd = viewport.getAlignment().getHiddenColumns()
1306             .getVisibleStartAndEndIndex(alignmentToExport.getWidth());
1307     AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
1308             omitHidden, alignmentStartEnd, settings);
1309     return ed;
1310   }
1311
1312   /**
1313    * DOCUMENT ME!
1314    *
1315    * @param e
1316    *          DOCUMENT ME!
1317    */
1318   @Override
1319   protected void htmlMenuItem_actionPerformed(ActionEvent e)
1320   {
1321     HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
1322     htmlSVG.exportHTML(null);
1323   }
1324
1325   @Override
1326   public void bioJSMenuItem_actionPerformed(ActionEvent e)
1327   {
1328     BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
1329     bjs.exportHTML(null);
1330   }
1331
1332   public void createImageMap(File file, String image)
1333   {
1334     alignPanel.makePNGImageMap(file, image);
1335   }
1336
1337   /**
1338    * DOCUMENT ME!
1339    *
1340    * @param e
1341    *          DOCUMENT ME!
1342    */
1343   @Override
1344   public void createPNG(File f)
1345   {
1346     alignPanel.makePNG(f);
1347   }
1348
1349   /**
1350    * DOCUMENT ME!
1351    *
1352    * @param e
1353    *          DOCUMENT ME!
1354    */
1355   @Override
1356   public void createEPS(File f)
1357   {
1358     alignPanel.makeEPS(f);
1359   }
1360
1361   @Override
1362   public void createSVG(File f)
1363   {
1364     alignPanel.makeSVG(f);
1365   }
1366
1367   @Override
1368   public void pageSetup_actionPerformed(ActionEvent e)
1369   {
1370     PrinterJob printJob = PrinterJob.getPrinterJob();
1371     PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1372   }
1373
1374   /**
1375    * DOCUMENT ME!
1376    *
1377    * @param e
1378    *          DOCUMENT ME!
1379    */
1380   @Override
1381   public void printMenuItem_actionPerformed(ActionEvent e)
1382   {
1383     // Putting in a thread avoids Swing painting problems
1384     PrintThread thread = new PrintThread(alignPanel);
1385     thread.start();
1386   }
1387
1388   @Override
1389   public void exportFeatures_actionPerformed(ActionEvent e)
1390   {
1391     new AnnotationExporter().exportFeatures(alignPanel);
1392   }
1393
1394   @Override
1395   public void exportAnnotations_actionPerformed(ActionEvent e)
1396   {
1397     new AnnotationExporter().exportAnnotations(alignPanel);
1398   }
1399
1400   @Override
1401   public void associatedData_actionPerformed(ActionEvent e)
1402   {
1403     // Pick the tree file
1404     JalviewFileChooser chooser = new JalviewFileChooser(
1405             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1406     chooser.setFileView(new JalviewFileView());
1407     chooser.setDialogTitle(
1408             MessageManager.getString("label.load_jalview_annotations"));
1409     chooser.setToolTipText(
1410             MessageManager.getString("label.load_jalview_annotations"));
1411
1412     int value = chooser.showOpenDialog(null);
1413
1414     if (value == JalviewFileChooser.APPROVE_OPTION)
1415     {
1416       String choice = chooser.getSelectedFile().getPath();
1417       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1418       loadJalviewDataFile(choice, null, null, null);
1419     }
1420
1421   }
1422
1423   /**
1424    * Close the current view or all views in the alignment frame. If the frame
1425    * only contains one view then the alignment will be removed from memory.
1426    *
1427    * @param closeAllTabs
1428    */
1429   @Override
1430   public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1431   {
1432     if (alignPanels != null && alignPanels.size() < 2)
1433     {
1434       closeAllTabs = true;
1435     }
1436
1437     try
1438     {
1439       if (alignPanels != null)
1440       {
1441         if (closeAllTabs)
1442         {
1443           if (this.isClosed())
1444           {
1445             // really close all the windows - otherwise wait till
1446             // setClosed(true) is called
1447             for (int i = 0; i < alignPanels.size(); i++)
1448             {
1449               AlignmentPanel ap = alignPanels.get(i);
1450               ap.closePanel();
1451             }
1452           }
1453         }
1454         else
1455         {
1456           closeView(alignPanel);
1457         }
1458       }
1459
1460       if (closeAllTabs)
1461       {
1462         /*
1463          * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1464          * be called recursively, with the frame now in 'closed' state
1465          */
1466         this.setClosed(true);
1467       }
1468     } catch (Exception ex)
1469     {
1470       ex.printStackTrace();
1471     }
1472   }
1473
1474   /**
1475    * Close the specified panel and close up tabs appropriately.
1476    *
1477    * @param panelToClose
1478    */
1479   public void closeView(AlignmentPanel panelToClose)
1480   {
1481     int index = tabbedPane.getSelectedIndex();
1482     int closedindex = tabbedPane.indexOfComponent(panelToClose);
1483     alignPanels.remove(panelToClose);
1484     panelToClose.closePanel();
1485     panelToClose = null;
1486
1487     tabbedPane.removeTabAt(closedindex);
1488     tabbedPane.validate();
1489
1490     if (index > closedindex || index == tabbedPane.getTabCount())
1491     {
1492       // modify currently selected tab index if necessary.
1493       index--;
1494     }
1495
1496     this.tabSelectionChanged(index);
1497   }
1498
1499   /**
1500    * DOCUMENT ME!
1501    */
1502   void updateEditMenuBar()
1503   {
1504
1505     if (viewport.getHistoryList().size() > 0)
1506     {
1507       undoMenuItem.setEnabled(true);
1508       CommandI command = viewport.getHistoryList().peek();
1509       undoMenuItem.setText(MessageManager
1510               .formatMessage("label.undo_command", new Object[]
1511               { command.getDescription() }));
1512     }
1513     else
1514     {
1515       undoMenuItem.setEnabled(false);
1516       undoMenuItem.setText(MessageManager.getString("action.undo"));
1517     }
1518
1519     if (viewport.getRedoList().size() > 0)
1520     {
1521       redoMenuItem.setEnabled(true);
1522
1523       CommandI command = viewport.getRedoList().peek();
1524       redoMenuItem.setText(MessageManager
1525               .formatMessage("label.redo_command", new Object[]
1526               { command.getDescription() }));
1527     }
1528     else
1529     {
1530       redoMenuItem.setEnabled(false);
1531       redoMenuItem.setText(MessageManager.getString("action.redo"));
1532     }
1533   }
1534
1535   @Override
1536   public void addHistoryItem(CommandI command)
1537   {
1538     if (command.getSize() > 0)
1539     {
1540       viewport.addToHistoryList(command);
1541       viewport.clearRedoList();
1542       updateEditMenuBar();
1543       viewport.updateHiddenColumns();
1544       // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1545       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1546       // viewport.getColumnSelection()
1547       // .getHiddenColumns().size() > 0);
1548     }
1549   }
1550
1551   /**
1552    *
1553    * @return alignment objects for all views
1554    */
1555   AlignmentI[] getViewAlignments()
1556   {
1557     if (alignPanels != null)
1558     {
1559       AlignmentI[] als = new AlignmentI[alignPanels.size()];
1560       int i = 0;
1561       for (AlignmentPanel ap : alignPanels)
1562       {
1563         als[i++] = ap.av.getAlignment();
1564       }
1565       return als;
1566     }
1567     if (viewport != null)
1568     {
1569       return new AlignmentI[] { viewport.getAlignment() };
1570     }
1571     return null;
1572   }
1573
1574   /**
1575    * DOCUMENT ME!
1576    *
1577    * @param e
1578    *          DOCUMENT ME!
1579    */
1580   @Override
1581   protected void undoMenuItem_actionPerformed(ActionEvent e)
1582   {
1583     if (viewport.getHistoryList().isEmpty())
1584     {
1585       return;
1586     }
1587     CommandI command = viewport.getHistoryList().pop();
1588     viewport.addToRedoList(command);
1589     command.undoCommand(getViewAlignments());
1590
1591     AlignmentViewport originalSource = getOriginatingSource(command);
1592     updateEditMenuBar();
1593
1594     if (originalSource != null)
1595     {
1596       if (originalSource != viewport)
1597       {
1598         Cache.log.warn(
1599                 "Implementation worry: mismatch of viewport origin for undo");
1600       }
1601       originalSource.updateHiddenColumns();
1602       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1603       // null
1604       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1605       // viewport.getColumnSelection()
1606       // .getHiddenColumns().size() > 0);
1607       originalSource.firePropertyChange("alignment", null,
1608               originalSource.getAlignment().getSequences());
1609     }
1610   }
1611
1612   /**
1613    * DOCUMENT ME!
1614    *
1615    * @param e
1616    *          DOCUMENT ME!
1617    */
1618   @Override
1619   protected void redoMenuItem_actionPerformed(ActionEvent e)
1620   {
1621     if (viewport.getRedoList().size() < 1)
1622     {
1623       return;
1624     }
1625
1626     CommandI command = viewport.getRedoList().pop();
1627     viewport.addToHistoryList(command);
1628     command.doCommand(getViewAlignments());
1629
1630     AlignmentViewport originalSource = getOriginatingSource(command);
1631     updateEditMenuBar();
1632
1633     if (originalSource != null)
1634     {
1635
1636       if (originalSource != viewport)
1637       {
1638         Cache.log.warn(
1639                 "Implementation worry: mismatch of viewport origin for redo");
1640       }
1641       originalSource.updateHiddenColumns();
1642       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1643       // null
1644       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1645       // viewport.getColumnSelection()
1646       // .getHiddenColumns().size() > 0);
1647       originalSource.firePropertyChange("alignment", null,
1648               originalSource.getAlignment().getSequences());
1649     }
1650   }
1651
1652   AlignmentViewport getOriginatingSource(CommandI command)
1653   {
1654     AlignmentViewport originalSource = null;
1655     // For sequence removal and addition, we need to fire
1656     // the property change event FROM the viewport where the
1657     // original alignment was altered
1658     AlignmentI al = null;
1659     if (command instanceof EditCommand)
1660     {
1661       EditCommand editCommand = (EditCommand) command;
1662       al = editCommand.getAlignment();
1663       List<Component> comps = PaintRefresher.components
1664               .get(viewport.getSequenceSetId());
1665
1666       for (Component comp : comps)
1667       {
1668         if (comp instanceof AlignmentPanel)
1669         {
1670           if (al == ((AlignmentPanel) comp).av.getAlignment())
1671           {
1672             originalSource = ((AlignmentPanel) comp).av;
1673             break;
1674           }
1675         }
1676       }
1677     }
1678
1679     if (originalSource == null)
1680     {
1681       // The original view is closed, we must validate
1682       // the current view against the closed view first
1683       if (al != null)
1684       {
1685         PaintRefresher.validateSequences(al, viewport.getAlignment());
1686       }
1687
1688       originalSource = viewport;
1689     }
1690
1691     return originalSource;
1692   }
1693
1694   /**
1695    * DOCUMENT ME!
1696    *
1697    * @param up
1698    *          DOCUMENT ME!
1699    */
1700   public void moveSelectedSequences(boolean up)
1701   {
1702     SequenceGroup sg = viewport.getSelectionGroup();
1703
1704     if (sg == null)
1705     {
1706       return;
1707     }
1708     viewport.getAlignment().moveSelectedSequencesByOne(sg,
1709             viewport.getHiddenRepSequences(), up);
1710     alignPanel.paintAlignment(true, false);
1711   }
1712
1713   synchronized void slideSequences(boolean right, int size)
1714   {
1715     List<SequenceI> sg = new ArrayList<>();
1716     if (viewport.cursorMode)
1717     {
1718       sg.add(viewport.getAlignment()
1719               .getSequenceAt(alignPanel.getSeqPanel().seqCanvas.cursorY));
1720     }
1721     else if (viewport.getSelectionGroup() != null
1722             && viewport.getSelectionGroup().getSize() != viewport
1723                     .getAlignment().getHeight())
1724     {
1725       sg = viewport.getSelectionGroup()
1726               .getSequences(viewport.getHiddenRepSequences());
1727     }
1728
1729     if (sg.size() < 1)
1730     {
1731       return;
1732     }
1733
1734     List<SequenceI> invertGroup = new ArrayList<>();
1735
1736     for (SequenceI seq : viewport.getAlignment().getSequences())
1737     {
1738       if (!sg.contains(seq))
1739       {
1740         invertGroup.add(seq);
1741       }
1742     }
1743
1744     SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1745
1746     SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1747     for (int i = 0; i < invertGroup.size(); i++)
1748     {
1749       seqs2[i] = invertGroup.get(i);
1750     }
1751
1752     SlideSequencesCommand ssc;
1753     if (right)
1754     {
1755       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1, size,
1756               viewport.getGapCharacter());
1757     }
1758     else
1759     {
1760       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2, size,
1761               viewport.getGapCharacter());
1762     }
1763
1764     int groupAdjustment = 0;
1765     if (ssc.getGapsInsertedBegin() && right)
1766     {
1767       if (viewport.cursorMode)
1768       {
1769         alignPanel.getSeqPanel().moveCursor(size, 0);
1770       }
1771       else
1772       {
1773         groupAdjustment = size;
1774       }
1775     }
1776     else if (!ssc.getGapsInsertedBegin() && !right)
1777     {
1778       if (viewport.cursorMode)
1779       {
1780         alignPanel.getSeqPanel().moveCursor(-size, 0);
1781       }
1782       else
1783       {
1784         groupAdjustment = -size;
1785       }
1786     }
1787
1788     if (groupAdjustment != 0)
1789     {
1790       viewport.getSelectionGroup().setStartRes(
1791               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1792       viewport.getSelectionGroup().setEndRes(
1793               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1794     }
1795
1796     /*
1797      * just extend the last slide command if compatible; but not if in
1798      * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1799      */
1800     boolean appendHistoryItem = false;
1801     Deque<CommandI> historyList = viewport.getHistoryList();
1802     boolean inSplitFrame = getSplitViewContainer() != null;
1803     if (!inSplitFrame && historyList != null && historyList.size() > 0
1804             && historyList.peek() instanceof SlideSequencesCommand)
1805     {
1806       appendHistoryItem = ssc.appendSlideCommand(
1807               (SlideSequencesCommand) historyList.peek());
1808     }
1809
1810     if (!appendHistoryItem)
1811     {
1812       addHistoryItem(ssc);
1813     }
1814
1815     repaint();
1816   }
1817
1818   /**
1819    * DOCUMENT ME!
1820    *
1821    * @param e
1822    *          DOCUMENT ME!
1823    */
1824   @Override
1825   protected void copy_actionPerformed(ActionEvent e)
1826   {
1827     System.gc();
1828     if (viewport.getSelectionGroup() == null)
1829     {
1830       return;
1831     }
1832     // TODO: preserve the ordering of displayed alignment annotation in any
1833     // internal paste (particularly sequence associated annotation)
1834     SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1835     String[] omitHidden = null;
1836
1837     if (viewport.hasHiddenColumns())
1838     {
1839       omitHidden = viewport.getViewAsString(true);
1840     }
1841
1842     String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
1843             seqs, omitHidden, null);
1844
1845     StringSelection ss = new StringSelection(output);
1846
1847     try
1848     {
1849       jalview.gui.Desktop.internalCopy = true;
1850       // Its really worth setting the clipboard contents
1851       // to empty before setting the large StringSelection!!
1852       Toolkit.getDefaultToolkit().getSystemClipboard()
1853               .setContents(new StringSelection(""), null);
1854
1855       Toolkit.getDefaultToolkit().getSystemClipboard().setContents(ss,
1856               Desktop.instance);
1857     } catch (OutOfMemoryError er)
1858     {
1859       new OOMWarning("copying region", er);
1860       return;
1861     }
1862
1863     ArrayList<int[]> hiddenColumns = null;
1864     if (viewport.hasHiddenColumns())
1865     {
1866       hiddenColumns = new ArrayList<>();
1867       int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1868       int hiddenCutoff = viewport.getSelectionGroup().getEndRes();
1869       ArrayList<int[]> hiddenRegions = viewport.getAlignment()
1870               .getHiddenColumns().getHiddenColumnsCopy();
1871       for (int[] region : hiddenRegions)
1872       {
1873         if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
1874         {
1875           hiddenColumns
1876                   .add(new int[]
1877                   { region[0] - hiddenOffset, region[1] - hiddenOffset });
1878         }
1879       }
1880     }
1881
1882     Desktop.jalviewClipboard = new Object[] { seqs,
1883         viewport.getAlignment().getDataset(), hiddenColumns };
1884     statusBar.setText(MessageManager.formatMessage(
1885             "label.copied_sequences_to_clipboard", new Object[]
1886             { Integer.valueOf(seqs.length).toString() }));
1887   }
1888
1889   /**
1890    * DOCUMENT ME!
1891    *
1892    * @param e
1893    *          DOCUMENT ME!
1894    */
1895   @Override
1896   protected void pasteNew_actionPerformed(ActionEvent e)
1897   {
1898     paste(true);
1899   }
1900
1901   /**
1902    * DOCUMENT ME!
1903    *
1904    * @param e
1905    *          DOCUMENT ME!
1906    */
1907   @Override
1908   protected void pasteThis_actionPerformed(ActionEvent e)
1909   {
1910     paste(false);
1911   }
1912
1913   /**
1914    * Paste contents of Jalview clipboard
1915    *
1916    * @param newAlignment
1917    *          true to paste to a new alignment, otherwise add to this.
1918    */
1919   void paste(boolean newAlignment)
1920   {
1921     boolean externalPaste = true;
1922     try
1923     {
1924       Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1925       Transferable contents = c.getContents(this);
1926
1927       if (contents == null)
1928       {
1929         return;
1930       }
1931
1932       String str;
1933       FileFormatI format;
1934       try
1935       {
1936         str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1937         if (str.length() < 1)
1938         {
1939           return;
1940         }
1941
1942         format = new IdentifyFile().identify(str, DataSourceType.PASTE);
1943
1944       } catch (OutOfMemoryError er)
1945       {
1946         new OOMWarning("Out of memory pasting sequences!!", er);
1947         return;
1948       }
1949
1950       SequenceI[] sequences;
1951       boolean annotationAdded = false;
1952       AlignmentI alignment = null;
1953
1954       if (Desktop.jalviewClipboard != null)
1955       {
1956         // The clipboard was filled from within Jalview, we must use the
1957         // sequences
1958         // And dataset from the copied alignment
1959         SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
1960         // be doubly sure that we create *new* sequence objects.
1961         sequences = new SequenceI[newseq.length];
1962         for (int i = 0; i < newseq.length; i++)
1963         {
1964           sequences[i] = new Sequence(newseq[i]);
1965         }
1966         alignment = new Alignment(sequences);
1967         externalPaste = false;
1968       }
1969       else
1970       {
1971         // parse the clipboard as an alignment.
1972         alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE,
1973                 format);
1974         sequences = alignment.getSequencesArray();
1975       }
1976
1977       int alwidth = 0;
1978       ArrayList<Integer> newGraphGroups = new ArrayList<>();
1979       int fgroup = -1;
1980
1981       if (newAlignment)
1982       {
1983
1984         if (Desktop.jalviewClipboard != null)
1985         {
1986           // dataset is inherited
1987           alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
1988         }
1989         else
1990         {
1991           // new dataset is constructed
1992           alignment.setDataset(null);
1993         }
1994         alwidth = alignment.getWidth() + 1;
1995       }
1996       else
1997       {
1998         AlignmentI pastedal = alignment; // preserve pasted alignment object
1999         // Add pasted sequences and dataset into existing alignment.
2000         alignment = viewport.getAlignment();
2001         alwidth = alignment.getWidth() + 1;
2002         // decide if we need to import sequences from an existing dataset
2003         boolean importDs = Desktop.jalviewClipboard != null
2004                 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2005         // importDs==true instructs us to copy over new dataset sequences from
2006         // an existing alignment
2007         Vector newDs = (importDs) ? new Vector() : null; // used to create
2008         // minimum dataset set
2009
2010         for (int i = 0; i < sequences.length; i++)
2011         {
2012           if (importDs)
2013           {
2014             newDs.addElement(null);
2015           }
2016           SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2017           // paste
2018           if (importDs && ds != null)
2019           {
2020             if (!newDs.contains(ds))
2021             {
2022               newDs.setElementAt(ds, i);
2023               ds = new Sequence(ds);
2024               // update with new dataset sequence
2025               sequences[i].setDatasetSequence(ds);
2026             }
2027             else
2028             {
2029               ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2030             }
2031           }
2032           else
2033           {
2034             // copy and derive new dataset sequence
2035             sequences[i] = sequences[i].deriveSequence();
2036             alignment.getDataset()
2037                     .addSequence(sequences[i].getDatasetSequence());
2038             // TODO: avoid creation of duplicate dataset sequences with a
2039             // 'contains' method using SequenceI.equals()/SequenceI.contains()
2040           }
2041           alignment.addSequence(sequences[i]); // merges dataset
2042         }
2043         if (newDs != null)
2044         {
2045           newDs.clear(); // tidy up
2046         }
2047         if (alignment.getAlignmentAnnotation() != null)
2048         {
2049           for (AlignmentAnnotation alan : alignment
2050                   .getAlignmentAnnotation())
2051           {
2052             if (alan.graphGroup > fgroup)
2053             {
2054               fgroup = alan.graphGroup;
2055             }
2056           }
2057         }
2058         if (pastedal.getAlignmentAnnotation() != null)
2059         {
2060           // Add any annotation attached to alignment.
2061           AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2062           for (int i = 0; i < alann.length; i++)
2063           {
2064             annotationAdded = true;
2065             if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2066             {
2067               AlignmentAnnotation newann = new AlignmentAnnotation(
2068                       alann[i]);
2069               if (newann.graphGroup > -1)
2070               {
2071                 if (newGraphGroups.size() <= newann.graphGroup
2072                         || newGraphGroups.get(newann.graphGroup) == null)
2073                 {
2074                   for (int q = newGraphGroups
2075                           .size(); q <= newann.graphGroup; q++)
2076                   {
2077                     newGraphGroups.add(q, null);
2078                   }
2079                   newGraphGroups.set(newann.graphGroup,
2080                           new Integer(++fgroup));
2081                 }
2082                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2083                         .intValue();
2084               }
2085
2086               newann.padAnnotation(alwidth);
2087               alignment.addAnnotation(newann);
2088             }
2089           }
2090         }
2091       }
2092       if (!newAlignment)
2093       {
2094         // /////
2095         // ADD HISTORY ITEM
2096         //
2097         addHistoryItem(new EditCommand(
2098                 MessageManager.getString("label.add_sequences"),
2099                 Action.PASTE, sequences, 0, alignment.getWidth(),
2100                 alignment));
2101       }
2102       // Add any annotations attached to sequences
2103       for (int i = 0; i < sequences.length; i++)
2104       {
2105         if (sequences[i].getAnnotation() != null)
2106         {
2107           AlignmentAnnotation newann;
2108           for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2109           {
2110             annotationAdded = true;
2111             newann = sequences[i].getAnnotation()[a];
2112             newann.adjustForAlignment();
2113             newann.padAnnotation(alwidth);
2114             if (newann.graphGroup > -1)
2115             {
2116               if (newann.graphGroup > -1)
2117               {
2118                 if (newGraphGroups.size() <= newann.graphGroup
2119                         || newGraphGroups.get(newann.graphGroup) == null)
2120                 {
2121                   for (int q = newGraphGroups
2122                           .size(); q <= newann.graphGroup; q++)
2123                   {
2124                     newGraphGroups.add(q, null);
2125                   }
2126                   newGraphGroups.set(newann.graphGroup,
2127                           new Integer(++fgroup));
2128                 }
2129                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2130                         .intValue();
2131               }
2132             }
2133             alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2134             // was
2135             // duplicated
2136             // earlier
2137             alignment.setAnnotationIndex(sequences[i].getAnnotation()[a],
2138                     a);
2139           }
2140         }
2141       }
2142       if (!newAlignment)
2143       {
2144
2145         // propagate alignment changed.
2146         viewport.getRanges().setEndSeq(alignment.getHeight());
2147         if (annotationAdded)
2148         {
2149           // Duplicate sequence annotation in all views.
2150           AlignmentI[] alview = this.getViewAlignments();
2151           for (int i = 0; i < sequences.length; i++)
2152           {
2153             AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2154             if (sann == null)
2155             {
2156               continue;
2157             }
2158             for (int avnum = 0; avnum < alview.length; avnum++)
2159             {
2160               if (alview[avnum] != alignment)
2161               {
2162                 // duplicate in a view other than the one with input focus
2163                 int avwidth = alview[avnum].getWidth() + 1;
2164                 // this relies on sann being preserved after we
2165                 // modify the sequence's annotation array for each duplication
2166                 for (int a = 0; a < sann.length; a++)
2167                 {
2168                   AlignmentAnnotation newann = new AlignmentAnnotation(
2169                           sann[a]);
2170                   sequences[i].addAlignmentAnnotation(newann);
2171                   newann.padAnnotation(avwidth);
2172                   alview[avnum].addAnnotation(newann); // annotation was
2173                   // duplicated earlier
2174                   // TODO JAL-1145 graphGroups are not updated for sequence
2175                   // annotation added to several views. This may cause
2176                   // strangeness
2177                   alview[avnum].setAnnotationIndex(newann, a);
2178                 }
2179               }
2180             }
2181           }
2182           buildSortByAnnotationScoresMenu();
2183         }
2184         viewport.firePropertyChange("alignment", null,
2185                 alignment.getSequences());
2186         if (alignPanels != null)
2187         {
2188           for (AlignmentPanel ap : alignPanels)
2189           {
2190             ap.validateAnnotationDimensions(false);
2191           }
2192         }
2193         else
2194         {
2195           alignPanel.validateAnnotationDimensions(false);
2196         }
2197
2198       }
2199       else
2200       {
2201         AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2202                 DEFAULT_HEIGHT);
2203         String newtitle = new String("Copied sequences");
2204
2205         if (Desktop.jalviewClipboard != null
2206                 && Desktop.jalviewClipboard[2] != null)
2207         {
2208           List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2209           for (int[] region : hc)
2210           {
2211             af.viewport.hideColumns(region[0], region[1]);
2212           }
2213         }
2214
2215         // >>>This is a fix for the moment, until a better solution is
2216         // found!!<<<
2217         af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2218                 .transferSettings(alignPanel.getSeqPanel().seqCanvas
2219                         .getFeatureRenderer());
2220
2221         // TODO: maintain provenance of an alignment, rather than just make the
2222         // title a concatenation of operations.
2223         if (!externalPaste)
2224         {
2225           if (title.startsWith("Copied sequences"))
2226           {
2227             newtitle = title;
2228           }
2229           else
2230           {
2231             newtitle = newtitle.concat("- from " + title);
2232           }
2233         }
2234         else
2235         {
2236           newtitle = new String("Pasted sequences");
2237         }
2238
2239         Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2240                 DEFAULT_HEIGHT);
2241
2242       }
2243
2244     } catch (Exception ex)
2245     {
2246       ex.printStackTrace();
2247       System.out.println("Exception whilst pasting: " + ex);
2248       // could be anything being pasted in here
2249     }
2250
2251   }
2252
2253   @Override
2254   protected void expand_newalign(ActionEvent e)
2255   {
2256     try
2257     {
2258       AlignmentI alignment = AlignmentUtils
2259               .expandContext(getViewport().getAlignment(), -1);
2260       AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2261               DEFAULT_HEIGHT);
2262       String newtitle = new String("Flanking alignment");
2263
2264       if (Desktop.jalviewClipboard != null
2265               && Desktop.jalviewClipboard[2] != null)
2266       {
2267         List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2268         for (int region[] : hc)
2269         {
2270           af.viewport.hideColumns(region[0], region[1]);
2271         }
2272       }
2273
2274       // >>>This is a fix for the moment, until a better solution is
2275       // found!!<<<
2276       af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2277               .transferSettings(alignPanel.getSeqPanel().seqCanvas
2278                       .getFeatureRenderer());
2279
2280       // TODO: maintain provenance of an alignment, rather than just make the
2281       // title a concatenation of operations.
2282       {
2283         if (title.startsWith("Copied sequences"))
2284         {
2285           newtitle = title;
2286         }
2287         else
2288         {
2289           newtitle = newtitle.concat("- from " + title);
2290         }
2291       }
2292
2293       Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2294
2295     } catch (Exception ex)
2296     {
2297       ex.printStackTrace();
2298       System.out.println("Exception whilst pasting: " + ex);
2299       // could be anything being pasted in here
2300     } catch (OutOfMemoryError oom)
2301     {
2302       new OOMWarning("Viewing flanking region of alignment", oom);
2303     }
2304   }
2305
2306   /**
2307    * DOCUMENT ME!
2308    *
2309    * @param e
2310    *          DOCUMENT ME!
2311    */
2312   @Override
2313   protected void cut_actionPerformed(ActionEvent e)
2314   {
2315     copy_actionPerformed(null);
2316     delete_actionPerformed(null);
2317   }
2318
2319   /**
2320    * DOCUMENT ME!
2321    *
2322    * @param e
2323    *          DOCUMENT ME!
2324    */
2325   @Override
2326   protected void delete_actionPerformed(ActionEvent evt)
2327   {
2328
2329     SequenceGroup sg = viewport.getSelectionGroup();
2330     if (sg == null)
2331     {
2332       return;
2333     }
2334
2335     /*
2336      * If the cut affects all sequences, warn, remove highlighted columns
2337      */
2338     if (sg.getSize() == viewport.getAlignment().getHeight())
2339     {
2340       boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes())
2341               + 1) == viewport.getAlignment().getWidth()) ? true : false;
2342       if (isEntireAlignWidth)
2343       {
2344         int confirm = JvOptionPane.showConfirmDialog(this,
2345                 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2346                 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2347                 JvOptionPane.OK_CANCEL_OPTION);
2348
2349         if (confirm == JvOptionPane.CANCEL_OPTION
2350                 || confirm == JvOptionPane.CLOSED_OPTION)
2351         {
2352           return;
2353         }
2354       }
2355       viewport.getColumnSelection().removeElements(sg.getStartRes(),
2356               sg.getEndRes() + 1);
2357     }
2358     SequenceI[] cut = sg.getSequences()
2359             .toArray(new SequenceI[sg.getSize()]);
2360
2361     addHistoryItem(new EditCommand(
2362             MessageManager.getString("label.cut_sequences"), Action.CUT,
2363             cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2364             viewport.getAlignment()));
2365
2366     viewport.setSelectionGroup(null);
2367     viewport.sendSelection();
2368     viewport.getAlignment().deleteGroup(sg);
2369
2370     viewport.firePropertyChange("alignment", null,
2371             viewport.getAlignment().getSequences());
2372     if (viewport.getAlignment().getHeight() < 1)
2373     {
2374       try
2375       {
2376         this.setClosed(true);
2377       } catch (Exception ex)
2378       {
2379       }
2380     }
2381   }
2382
2383   /**
2384    * DOCUMENT ME!
2385    *
2386    * @param e
2387    *          DOCUMENT ME!
2388    */
2389   @Override
2390   protected void deleteGroups_actionPerformed(ActionEvent e)
2391   {
2392     if (avc.deleteGroups())
2393     {
2394       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2395       alignPanel.updateAnnotation();
2396       alignPanel.paintAlignment(true, true);
2397     }
2398   }
2399
2400   /**
2401    * DOCUMENT ME!
2402    *
2403    * @param e
2404    *          DOCUMENT ME!
2405    */
2406   @Override
2407   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2408   {
2409     SequenceGroup sg = new SequenceGroup();
2410
2411     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2412     {
2413       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2414     }
2415
2416     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2417     viewport.setSelectionGroup(sg);
2418     viewport.sendSelection();
2419     // JAL-2034 - should delegate to
2420     // alignPanel to decide if overview needs
2421     // updating.
2422     alignPanel.paintAlignment(false, false);
2423     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2424   }
2425
2426   /**
2427    * DOCUMENT ME!
2428    *
2429    * @param e
2430    *          DOCUMENT ME!
2431    */
2432   @Override
2433   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2434   {
2435     if (viewport.cursorMode)
2436     {
2437       alignPanel.getSeqPanel().keyboardNo1 = null;
2438       alignPanel.getSeqPanel().keyboardNo2 = null;
2439     }
2440     viewport.setSelectionGroup(null);
2441     viewport.getColumnSelection().clear();
2442     viewport.setSelectionGroup(null);
2443     alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2444     // JAL-2034 - should delegate to
2445     // alignPanel to decide if overview needs
2446     // updating.
2447     alignPanel.paintAlignment(false, false);
2448     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2449     viewport.sendSelection();
2450   }
2451
2452   /**
2453    * DOCUMENT ME!
2454    *
2455    * @param e
2456    *          DOCUMENT ME!
2457    */
2458   @Override
2459   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2460   {
2461     SequenceGroup sg = viewport.getSelectionGroup();
2462
2463     if (sg == null)
2464     {
2465       selectAllSequenceMenuItem_actionPerformed(null);
2466
2467       return;
2468     }
2469
2470     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2471     {
2472       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2473     }
2474     // JAL-2034 - should delegate to
2475     // alignPanel to decide if overview needs
2476     // updating.
2477
2478     alignPanel.paintAlignment(true, false);
2479     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2480     viewport.sendSelection();
2481   }
2482
2483   @Override
2484   public void invertColSel_actionPerformed(ActionEvent e)
2485   {
2486     viewport.invertColumnSelection();
2487     alignPanel.paintAlignment(true, false);
2488     viewport.sendSelection();
2489   }
2490
2491   /**
2492    * DOCUMENT ME!
2493    *
2494    * @param e
2495    *          DOCUMENT ME!
2496    */
2497   @Override
2498   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2499   {
2500     trimAlignment(true);
2501   }
2502
2503   /**
2504    * DOCUMENT ME!
2505    *
2506    * @param e
2507    *          DOCUMENT ME!
2508    */
2509   @Override
2510   public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2511   {
2512     trimAlignment(false);
2513   }
2514
2515   void trimAlignment(boolean trimLeft)
2516   {
2517     ColumnSelection colSel = viewport.getColumnSelection();
2518     int column;
2519
2520     if (!colSel.isEmpty())
2521     {
2522       if (trimLeft)
2523       {
2524         column = colSel.getMin();
2525       }
2526       else
2527       {
2528         column = colSel.getMax();
2529       }
2530
2531       SequenceI[] seqs;
2532       if (viewport.getSelectionGroup() != null)
2533       {
2534         seqs = viewport.getSelectionGroup()
2535                 .getSequencesAsArray(viewport.getHiddenRepSequences());
2536       }
2537       else
2538       {
2539         seqs = viewport.getAlignment().getSequencesArray();
2540       }
2541
2542       TrimRegionCommand trimRegion;
2543       if (trimLeft)
2544       {
2545         trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2546                 column, viewport.getAlignment());
2547         viewport.getRanges().setStartRes(0);
2548       }
2549       else
2550       {
2551         trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2552                 column, viewport.getAlignment());
2553       }
2554
2555       statusBar.setText(MessageManager
2556               .formatMessage("label.removed_columns", new String[]
2557               { Integer.valueOf(trimRegion.getSize()).toString() }));
2558
2559       addHistoryItem(trimRegion);
2560
2561       for (SequenceGroup sg : viewport.getAlignment().getGroups())
2562       {
2563         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2564                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2565         {
2566           viewport.getAlignment().deleteGroup(sg);
2567         }
2568       }
2569
2570       viewport.firePropertyChange("alignment", null,
2571               viewport.getAlignment().getSequences());
2572     }
2573   }
2574
2575   /**
2576    * DOCUMENT ME!
2577    *
2578    * @param e
2579    *          DOCUMENT ME!
2580    */
2581   @Override
2582   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2583   {
2584     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2585
2586     SequenceI[] seqs;
2587     if (viewport.getSelectionGroup() != null)
2588     {
2589       seqs = viewport.getSelectionGroup()
2590               .getSequencesAsArray(viewport.getHiddenRepSequences());
2591       start = viewport.getSelectionGroup().getStartRes();
2592       end = viewport.getSelectionGroup().getEndRes();
2593     }
2594     else
2595     {
2596       seqs = viewport.getAlignment().getSequencesArray();
2597     }
2598
2599     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2600             "Remove Gapped Columns", seqs, start, end,
2601             viewport.getAlignment());
2602
2603     addHistoryItem(removeGapCols);
2604
2605     statusBar.setText(MessageManager
2606             .formatMessage("label.removed_empty_columns", new Object[]
2607             { Integer.valueOf(removeGapCols.getSize()).toString() }));
2608
2609     // This is to maintain viewport position on first residue
2610     // of first sequence
2611     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2612     ViewportRanges ranges = viewport.getRanges();
2613     int startRes = seq.findPosition(ranges.getStartRes());
2614     // ShiftList shifts;
2615     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2616     // edit.alColumnChanges=shifts.getInverse();
2617     // if (viewport.hasHiddenColumns)
2618     // viewport.getColumnSelection().compensateForEdits(shifts);
2619     ranges.setStartRes(seq.findIndex(startRes) - 1);
2620     viewport.firePropertyChange("alignment", null,
2621             viewport.getAlignment().getSequences());
2622
2623   }
2624
2625   /**
2626    * DOCUMENT ME!
2627    *
2628    * @param e
2629    *          DOCUMENT ME!
2630    */
2631   @Override
2632   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2633   {
2634     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2635
2636     SequenceI[] seqs;
2637     if (viewport.getSelectionGroup() != null)
2638     {
2639       seqs = viewport.getSelectionGroup()
2640               .getSequencesAsArray(viewport.getHiddenRepSequences());
2641       start = viewport.getSelectionGroup().getStartRes();
2642       end = viewport.getSelectionGroup().getEndRes();
2643     }
2644     else
2645     {
2646       seqs = viewport.getAlignment().getSequencesArray();
2647     }
2648
2649     // This is to maintain viewport position on first residue
2650     // of first sequence
2651     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2652     int startRes = seq.findPosition(viewport.getRanges().getStartRes());
2653
2654     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2655             viewport.getAlignment()));
2656
2657     viewport.getRanges().setStartRes(seq.findIndex(startRes) - 1);
2658
2659     viewport.firePropertyChange("alignment", null,
2660             viewport.getAlignment().getSequences());
2661
2662   }
2663
2664   /**
2665    * DOCUMENT ME!
2666    *
2667    * @param e
2668    *          DOCUMENT ME!
2669    */
2670   @Override
2671   public void padGapsMenuitem_actionPerformed(ActionEvent e)
2672   {
2673     viewport.setPadGaps(padGapsMenuitem.isSelected());
2674     viewport.firePropertyChange("alignment", null,
2675             viewport.getAlignment().getSequences());
2676   }
2677
2678   /**
2679    * DOCUMENT ME!
2680    *
2681    * @param e
2682    *          DOCUMENT ME!
2683    */
2684   @Override
2685   public void findMenuItem_actionPerformed(ActionEvent e)
2686   {
2687     new Finder();
2688   }
2689
2690   /**
2691    * Create a new view of the current alignment.
2692    */
2693   @Override
2694   public void newView_actionPerformed(ActionEvent e)
2695   {
2696     newView(null, true);
2697   }
2698
2699   /**
2700    * Creates and shows a new view of the current alignment.
2701    *
2702    * @param viewTitle
2703    *          title of newly created view; if null, one will be generated
2704    * @param copyAnnotation
2705    *          if true then duplicate all annnotation, groups and settings
2706    * @return new alignment panel, already displayed.
2707    */
2708   public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2709   {
2710     /*
2711      * Create a new AlignmentPanel (with its own, new Viewport)
2712      */
2713     AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel);
2714     if (!copyAnnotation)
2715     {
2716       /*
2717        * remove all groups and annotation except for the automatic stuff
2718        */
2719       newap.av.getAlignment().deleteAllGroups();
2720       newap.av.getAlignment().deleteAllAnnotations(false);
2721     }
2722
2723     newap.av.setGatherViewsHere(false);
2724
2725     if (viewport.viewName == null)
2726     {
2727       viewport.viewName = MessageManager
2728               .getString("label.view_name_original");
2729     }
2730
2731     /*
2732      * Views share the same edits undo and redo stacks
2733      */
2734     newap.av.setHistoryList(viewport.getHistoryList());
2735     newap.av.setRedoList(viewport.getRedoList());
2736
2737     /*
2738      * Views share the same mappings; need to deregister any new mappings
2739      * created by copyAlignPanel, and register the new reference to the shared
2740      * mappings
2741      */
2742     newap.av.replaceMappings(viewport.getAlignment());
2743
2744     /*
2745      * start up cDNA consensus (if applicable) now mappings are in place
2746      */
2747     if (newap.av.initComplementConsensus())
2748     {
2749       newap.refresh(true); // adjust layout of annotations
2750     }
2751
2752     newap.av.viewName = getNewViewName(viewTitle);
2753
2754     addAlignmentPanel(newap, true);
2755     newap.alignmentChanged();
2756
2757     if (alignPanels.size() == 2)
2758     {
2759       viewport.setGatherViewsHere(true);
2760     }
2761     tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2762     return newap;
2763   }
2764
2765   /**
2766    * Make a new name for the view, ensuring it is unique within the current
2767    * sequenceSetId. (This used to be essential for Jalview Project archives, but
2768    * these now use viewId. Unique view names are still desirable for usability.)
2769    *
2770    * @param viewTitle
2771    * @return
2772    */
2773   protected String getNewViewName(String viewTitle)
2774   {
2775     int index = Desktop.getViewCount(viewport.getSequenceSetId());
2776     boolean addFirstIndex = false;
2777     if (viewTitle == null || viewTitle.trim().length() == 0)
2778     {
2779       viewTitle = MessageManager.getString("action.view");
2780       addFirstIndex = true;
2781     }
2782     else
2783     {
2784       index = 1;// we count from 1 if given a specific name
2785     }
2786     String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2787
2788     List<Component> comps = PaintRefresher.components
2789             .get(viewport.getSequenceSetId());
2790
2791     List<String> existingNames = getExistingViewNames(comps);
2792
2793     while (existingNames.contains(newViewName))
2794     {
2795       newViewName = viewTitle + " " + (++index);
2796     }
2797     return newViewName;
2798   }
2799
2800   /**
2801    * Returns a list of distinct view names found in the given list of
2802    * components. View names are held on the viewport of an AlignmentPanel.
2803    *
2804    * @param comps
2805    * @return
2806    */
2807   protected List<String> getExistingViewNames(List<Component> comps)
2808   {
2809     List<String> existingNames = new ArrayList<>();
2810     for (Component comp : comps)
2811     {
2812       if (comp instanceof AlignmentPanel)
2813       {
2814         AlignmentPanel ap = (AlignmentPanel) comp;
2815         if (!existingNames.contains(ap.av.viewName))
2816         {
2817           existingNames.add(ap.av.viewName);
2818         }
2819       }
2820     }
2821     return existingNames;
2822   }
2823
2824   /**
2825    * Explode tabbed views into separate windows.
2826    */
2827   @Override
2828   public void expandViews_actionPerformed(ActionEvent e)
2829   {
2830     Desktop.explodeViews(this);
2831   }
2832
2833   /**
2834    * Gather views in separate windows back into a tabbed presentation.
2835    */
2836   @Override
2837   public void gatherViews_actionPerformed(ActionEvent e)
2838   {
2839     Desktop.instance.gatherViews(this);
2840   }
2841
2842   /**
2843    * DOCUMENT ME!
2844    *
2845    * @param e
2846    *          DOCUMENT ME!
2847    */
2848   @Override
2849   public void font_actionPerformed(ActionEvent e)
2850   {
2851     new FontChooser(alignPanel);
2852   }
2853
2854   /**
2855    * DOCUMENT ME!
2856    *
2857    * @param e
2858    *          DOCUMENT ME!
2859    */
2860   @Override
2861   protected void seqLimit_actionPerformed(ActionEvent e)
2862   {
2863     viewport.setShowJVSuffix(seqLimits.isSelected());
2864
2865     alignPanel.getIdPanel().getIdCanvas()
2866             .setPreferredSize(alignPanel.calculateIdWidth());
2867     alignPanel.paintAlignment(true, false);
2868   }
2869
2870   @Override
2871   public void idRightAlign_actionPerformed(ActionEvent e)
2872   {
2873     viewport.setRightAlignIds(idRightAlign.isSelected());
2874     alignPanel.paintAlignment(false, false);
2875   }
2876
2877   @Override
2878   public void centreColumnLabels_actionPerformed(ActionEvent e)
2879   {
2880     viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2881     alignPanel.paintAlignment(false, false);
2882   }
2883
2884   /*
2885    * (non-Javadoc)
2886    *
2887    * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2888    */
2889   @Override
2890   protected void followHighlight_actionPerformed()
2891   {
2892     /*
2893      * Set the 'follow' flag on the Viewport (and scroll to position if now
2894      * true).
2895      */
2896     final boolean state = this.followHighlightMenuItem.getState();
2897     viewport.setFollowHighlight(state);
2898     if (state)
2899     {
2900       alignPanel.scrollToPosition(viewport.getSearchResults(), false);
2901     }
2902   }
2903
2904   /**
2905    * DOCUMENT ME!
2906    *
2907    * @param e
2908    *          DOCUMENT ME!
2909    */
2910   @Override
2911   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2912   {
2913     viewport.setColourText(colourTextMenuItem.isSelected());
2914     alignPanel.paintAlignment(false, false);
2915   }
2916
2917   /**
2918    * DOCUMENT ME!
2919    *
2920    * @param e
2921    *          DOCUMENT ME!
2922    */
2923   @Override
2924   public void wrapMenuItem_actionPerformed(ActionEvent e)
2925   {
2926     scaleAbove.setVisible(wrapMenuItem.isSelected());
2927     scaleLeft.setVisible(wrapMenuItem.isSelected());
2928     scaleRight.setVisible(wrapMenuItem.isSelected());
2929     viewport.setWrapAlignment(wrapMenuItem.isSelected());
2930     alignPanel.updateLayout();
2931   }
2932
2933   @Override
2934   public void showAllSeqs_actionPerformed(ActionEvent e)
2935   {
2936     viewport.showAllHiddenSeqs();
2937   }
2938
2939   @Override
2940   public void showAllColumns_actionPerformed(ActionEvent e)
2941   {
2942     viewport.showAllHiddenColumns();
2943     alignPanel.paintAlignment(true, true);
2944     viewport.sendSelection();
2945   }
2946
2947   @Override
2948   public void hideSelSequences_actionPerformed(ActionEvent e)
2949   {
2950     viewport.hideAllSelectedSeqs();
2951   }
2952
2953   /**
2954    * called by key handler and the hide all/show all menu items
2955    *
2956    * @param toggleSeqs
2957    * @param toggleCols
2958    */
2959   private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2960   {
2961
2962     boolean hide = false;
2963     SequenceGroup sg = viewport.getSelectionGroup();
2964     if (!toggleSeqs && !toggleCols)
2965     {
2966       // Hide everything by the current selection - this is a hack - we do the
2967       // invert and then hide
2968       // first check that there will be visible columns after the invert.
2969       if (viewport.hasSelectedColumns() || (sg != null && sg.getSize() > 0
2970               && sg.getStartRes() <= sg.getEndRes()))
2971       {
2972         // now invert the sequence set, if required - empty selection implies
2973         // that no hiding is required.
2974         if (sg != null)
2975         {
2976           invertSequenceMenuItem_actionPerformed(null);
2977           sg = viewport.getSelectionGroup();
2978           toggleSeqs = true;
2979
2980         }
2981         viewport.expandColSelection(sg, true);
2982         // finally invert the column selection and get the new sequence
2983         // selection.
2984         invertColSel_actionPerformed(null);
2985         toggleCols = true;
2986       }
2987     }
2988
2989     if (toggleSeqs)
2990     {
2991       if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
2992       {
2993         hideSelSequences_actionPerformed(null);
2994         hide = true;
2995       }
2996       else if (!(toggleCols && viewport.hasSelectedColumns()))
2997       {
2998         showAllSeqs_actionPerformed(null);
2999       }
3000     }
3001
3002     if (toggleCols)
3003     {
3004       if (viewport.hasSelectedColumns())
3005       {
3006         hideSelColumns_actionPerformed(null);
3007         if (!toggleSeqs)
3008         {
3009           viewport.setSelectionGroup(sg);
3010         }
3011       }
3012       else if (!hide)
3013       {
3014         showAllColumns_actionPerformed(null);
3015       }
3016     }
3017   }
3018
3019   /*
3020    * (non-Javadoc)
3021    *
3022    * @see
3023    * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3024    * event.ActionEvent)
3025    */
3026   @Override
3027   public void hideAllButSelection_actionPerformed(ActionEvent e)
3028   {
3029     toggleHiddenRegions(false, false);
3030     viewport.sendSelection();
3031   }
3032
3033   /*
3034    * (non-Javadoc)
3035    *
3036    * @see
3037    * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3038    * .ActionEvent)
3039    */
3040   @Override
3041   public void hideAllSelection_actionPerformed(ActionEvent e)
3042   {
3043     SequenceGroup sg = viewport.getSelectionGroup();
3044     viewport.expandColSelection(sg, false);
3045     viewport.hideAllSelectedSeqs();
3046     viewport.hideSelectedColumns();
3047     alignPanel.paintAlignment(true, true);
3048     viewport.sendSelection();
3049   }
3050
3051   /*
3052    * (non-Javadoc)
3053    *
3054    * @see
3055    * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3056    * ActionEvent)
3057    */
3058   @Override
3059   public void showAllhidden_actionPerformed(ActionEvent e)
3060   {
3061     viewport.showAllHiddenColumns();
3062     viewport.showAllHiddenSeqs();
3063     alignPanel.paintAlignment(true, true);
3064     viewport.sendSelection();
3065   }
3066
3067   @Override
3068   public void hideSelColumns_actionPerformed(ActionEvent e)
3069   {
3070     viewport.hideSelectedColumns();
3071     alignPanel.paintAlignment(true, true);
3072     viewport.sendSelection();
3073   }
3074
3075   @Override
3076   public void hiddenMarkers_actionPerformed(ActionEvent e)
3077   {
3078     viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3079     repaint();
3080   }
3081
3082   /**
3083    * DOCUMENT ME!
3084    *
3085    * @param e
3086    *          DOCUMENT ME!
3087    */
3088   @Override
3089   protected void scaleAbove_actionPerformed(ActionEvent e)
3090   {
3091     viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3092     // TODO: do we actually need to update overview for scale above change ?
3093     alignPanel.paintAlignment(true, false);
3094   }
3095
3096   /**
3097    * DOCUMENT ME!
3098    *
3099    * @param e
3100    *          DOCUMENT ME!
3101    */
3102   @Override
3103   protected void scaleLeft_actionPerformed(ActionEvent e)
3104   {
3105     viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3106     alignPanel.paintAlignment(true, false);
3107   }
3108
3109   /**
3110    * DOCUMENT ME!
3111    *
3112    * @param e
3113    *          DOCUMENT ME!
3114    */
3115   @Override
3116   protected void scaleRight_actionPerformed(ActionEvent e)
3117   {
3118     viewport.setScaleRightWrapped(scaleRight.isSelected());
3119     alignPanel.paintAlignment(true, false);
3120   }
3121
3122   /**
3123    * DOCUMENT ME!
3124    *
3125    * @param e
3126    *          DOCUMENT ME!
3127    */
3128   @Override
3129   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3130   {
3131     viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3132     alignPanel.paintAlignment(false, false);
3133   }
3134
3135   /**
3136    * DOCUMENT ME!
3137    *
3138    * @param e
3139    *          DOCUMENT ME!
3140    */
3141   @Override
3142   public void viewTextMenuItem_actionPerformed(ActionEvent e)
3143   {
3144     viewport.setShowText(viewTextMenuItem.isSelected());
3145     alignPanel.paintAlignment(false, false);
3146   }
3147
3148   /**
3149    * DOCUMENT ME!
3150    *
3151    * @param e
3152    *          DOCUMENT ME!
3153    */
3154   @Override
3155   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3156   {
3157     viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3158     alignPanel.paintAlignment(false, false);
3159   }
3160
3161   public FeatureSettings featureSettings;
3162
3163   @Override
3164   public FeatureSettingsControllerI getFeatureSettingsUI()
3165   {
3166     return featureSettings;
3167   }
3168
3169   @Override
3170   public void featureSettings_actionPerformed(ActionEvent e)
3171   {
3172     if (featureSettings != null)
3173     {
3174       featureSettings.close();
3175       featureSettings = null;
3176     }
3177     if (!showSeqFeatures.isSelected())
3178     {
3179       // make sure features are actually displayed
3180       showSeqFeatures.setSelected(true);
3181       showSeqFeatures_actionPerformed(null);
3182     }
3183     featureSettings = new FeatureSettings(this);
3184   }
3185
3186   /**
3187    * Set or clear 'Show Sequence Features'
3188    *
3189    * @param evt
3190    *          DOCUMENT ME!
3191    */
3192   @Override
3193   public void showSeqFeatures_actionPerformed(ActionEvent evt)
3194   {
3195     viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3196     alignPanel.paintAlignment(true, true);
3197   }
3198
3199   /**
3200    * Action on toggle of the 'Show annotations' menu item. This shows or hides
3201    * the annotations panel as a whole.
3202    *
3203    * The options to show/hide all annotations should be enabled when the panel
3204    * is shown, and disabled when the panel is hidden.
3205    *
3206    * @param e
3207    */
3208   @Override
3209   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3210   {
3211     final boolean setVisible = annotationPanelMenuItem.isSelected();
3212     viewport.setShowAnnotation(setVisible);
3213     this.showAllSeqAnnotations.setEnabled(setVisible);
3214     this.hideAllSeqAnnotations.setEnabled(setVisible);
3215     this.showAllAlAnnotations.setEnabled(setVisible);
3216     this.hideAllAlAnnotations.setEnabled(setVisible);
3217     alignPanel.updateLayout();
3218   }
3219
3220   @Override
3221   public void alignmentProperties()
3222   {
3223     CutAndPasteHtmlTransfer cap = new CutAndPasteHtmlTransfer();
3224     StringBuilder contents = new AlignmentProperties(
3225             viewport.getAlignment())
3226             .formatAsHtml();
3227     cap.setText("<html>" + contents.toString() + "</html>");
3228
3229     Desktop.addInternalFrame(cap, MessageManager
3230             .formatMessage("label.alignment_properties", new Object[]
3231             { getTitle() }), 500, 400);
3232   }
3233
3234   /**
3235    * DOCUMENT ME!
3236    *
3237    * @param e
3238    *          DOCUMENT ME!
3239    */
3240   @Override
3241   public void overviewMenuItem_actionPerformed(ActionEvent e)
3242   {
3243     if (alignPanel.overviewPanel != null)
3244     {
3245       return;
3246     }
3247
3248     JInternalFrame frame = new JInternalFrame();
3249     final OverviewPanel overview = new OverviewPanel(alignPanel);
3250     frame.setContentPane(overview);
3251     Desktop.addInternalFrame(frame, MessageManager
3252             .formatMessage("label.overview_params", new Object[]
3253             { this.getTitle() }), true, frame.getWidth(), frame.getHeight(),
3254             true, true);
3255     frame.pack();
3256     frame.setLayer(JLayeredPane.PALETTE_LAYER);
3257     frame.addInternalFrameListener(
3258             new javax.swing.event.InternalFrameAdapter()
3259             {
3260               @Override
3261               public void internalFrameClosed(
3262                       javax.swing.event.InternalFrameEvent evt)
3263               {
3264                 overview.dispose();
3265                 alignPanel.setOverviewPanel(null);
3266               };
3267             });
3268
3269     alignPanel.setOverviewPanel(overview);
3270   }
3271
3272   @Override
3273   public void textColour_actionPerformed()
3274   {
3275     new TextColourChooser().chooseColour(alignPanel, null);
3276   }
3277
3278   /*
3279    * public void covariationColour_actionPerformed() {
3280    * changeColour(new
3281    * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3282    * ()[0])); }
3283    */
3284   @Override
3285   public void annotationColour_actionPerformed()
3286   {
3287     new AnnotationColourChooser(viewport, alignPanel);
3288   }
3289
3290   @Override
3291   public void annotationColumn_actionPerformed(ActionEvent e)
3292   {
3293     new AnnotationColumnChooser(viewport, alignPanel);
3294   }
3295
3296   /**
3297    * Action on the user checking or unchecking the option to apply the selected
3298    * colour scheme to all groups. If unchecked, groups may have their own
3299    * independent colour schemes.
3300    *
3301    * @param selected
3302    */
3303   @Override
3304   public void applyToAllGroups_actionPerformed(boolean selected)
3305   {
3306     viewport.setColourAppliesToAllGroups(selected);
3307   }
3308
3309   /**
3310    * Action on user selecting a colour from the colour menu
3311    *
3312    * @param name
3313    *          the name (not the menu item label!) of the colour scheme
3314    */
3315   @Override
3316   public void changeColour_actionPerformed(String name)
3317   {
3318     /*
3319      * 'User Defined' opens a panel to configure or load a
3320      * user-defined colour scheme
3321      */
3322     if (ResidueColourScheme.USER_DEFINED_MENU.equals(name))
3323     {
3324       new UserDefinedColours(alignPanel);
3325       return;
3326     }
3327
3328     /*
3329      * otherwise set the chosen colour scheme (or null for 'None')
3330      */
3331     ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
3332             viewport.getAlignment(), viewport.getHiddenRepSequences());
3333     changeColour(cs);
3334   }
3335
3336   /**
3337    * Actions on setting or changing the alignment colour scheme
3338    *
3339    * @param cs
3340    */
3341   @Override
3342   public void changeColour(ColourSchemeI cs)
3343   {
3344     // TODO: pull up to controller method
3345     ColourMenuHelper.setColourSelected(colourMenu, cs);
3346
3347     viewport.setGlobalColourScheme(cs);
3348
3349     alignPanel.paintAlignment(true, true);
3350   }
3351
3352   /**
3353    * Show the PID threshold slider panel
3354    */
3355   @Override
3356   protected void modifyPID_actionPerformed()
3357   {
3358     SliderPanel.setPIDSliderSource(alignPanel, viewport.getResidueShading(),
3359             alignPanel.getViewName());
3360     SliderPanel.showPIDSlider();
3361   }
3362
3363   /**
3364    * Show the Conservation slider panel
3365    */
3366   @Override
3367   protected void modifyConservation_actionPerformed()
3368   {
3369     SliderPanel.setConservationSlider(alignPanel,
3370             viewport.getResidueShading(), alignPanel.getViewName());
3371     SliderPanel.showConservationSlider();
3372   }
3373
3374   /**
3375    * Action on selecting or deselecting (Colour) By Conservation
3376    */
3377   @Override
3378   public void conservationMenuItem_actionPerformed(boolean selected)
3379   {
3380     modifyConservation.setEnabled(selected);
3381     viewport.setConservationSelected(selected);
3382     viewport.getResidueShading().setConservationApplied(selected);
3383
3384     changeColour(viewport.getGlobalColourScheme());
3385     if (selected)
3386     {
3387       modifyConservation_actionPerformed();
3388     }
3389     else
3390     {
3391       SliderPanel.hideConservationSlider();
3392     }
3393   }
3394
3395   /**
3396    * Action on selecting or deselecting (Colour) Above PID Threshold
3397    */
3398   @Override
3399   public void abovePIDThreshold_actionPerformed(boolean selected)
3400   {
3401     modifyPID.setEnabled(selected);
3402     viewport.setAbovePIDThreshold(selected);
3403     if (!selected)
3404     {
3405       viewport.getResidueShading().setThreshold(0,
3406               viewport.isIgnoreGapsConsensus());
3407     }
3408
3409     changeColour(viewport.getGlobalColourScheme());
3410     if (selected)
3411     {
3412       modifyPID_actionPerformed();
3413     }
3414     else
3415     {
3416       SliderPanel.hidePIDSlider();
3417     }
3418   }
3419
3420   /**
3421    * DOCUMENT ME!
3422    *
3423    * @param e
3424    *          DOCUMENT ME!
3425    */
3426   @Override
3427   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3428   {
3429     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3430     AlignmentSorter.sortByPID(viewport.getAlignment(),
3431             viewport.getAlignment().getSequenceAt(0));
3432     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3433             viewport.getAlignment()));
3434     alignPanel.paintAlignment(true, false);
3435   }
3436
3437   /**
3438    * DOCUMENT ME!
3439    *
3440    * @param e
3441    *          DOCUMENT ME!
3442    */
3443   @Override
3444   public void sortIDMenuItem_actionPerformed(ActionEvent e)
3445   {
3446     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3447     AlignmentSorter.sortByID(viewport.getAlignment());
3448     addHistoryItem(
3449             new OrderCommand("ID Sort", oldOrder, viewport.getAlignment()));
3450     alignPanel.paintAlignment(true, false);
3451   }
3452
3453   /**
3454    * DOCUMENT ME!
3455    *
3456    * @param e
3457    *          DOCUMENT ME!
3458    */
3459   @Override
3460   public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3461   {
3462     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3463     AlignmentSorter.sortByLength(viewport.getAlignment());
3464     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3465             viewport.getAlignment()));
3466     alignPanel.paintAlignment(true, false);
3467   }
3468
3469   /**
3470    * DOCUMENT ME!
3471    *
3472    * @param e
3473    *          DOCUMENT ME!
3474    */
3475   @Override
3476   public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3477   {
3478     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3479     AlignmentSorter.sortByGroup(viewport.getAlignment());
3480     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3481             viewport.getAlignment()));
3482
3483     alignPanel.paintAlignment(true, false);
3484   }
3485
3486   /**
3487    * DOCUMENT ME!
3488    *
3489    * @param e
3490    *          DOCUMENT ME!
3491    */
3492   @Override
3493   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3494   {
3495     new RedundancyPanel(alignPanel, this);
3496   }
3497
3498   /**
3499    * DOCUMENT ME!
3500    *
3501    * @param e
3502    *          DOCUMENT ME!
3503    */
3504   @Override
3505   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3506   {
3507     if ((viewport.getSelectionGroup() == null)
3508             || (viewport.getSelectionGroup().getSize() < 2))
3509     {
3510       JvOptionPane.showInternalMessageDialog(this,
3511               MessageManager.getString(
3512                       "label.you_must_select_least_two_sequences"),
3513               MessageManager.getString("label.invalid_selection"),
3514               JvOptionPane.WARNING_MESSAGE);
3515     }
3516     else
3517     {
3518       JInternalFrame frame = new JInternalFrame();
3519       frame.setContentPane(new PairwiseAlignPanel(viewport));
3520       Desktop.addInternalFrame(frame,
3521               MessageManager.getString("action.pairwise_alignment"), 600,
3522               500);
3523     }
3524   }
3525
3526   @Override
3527   public void autoCalculate_actionPerformed(ActionEvent e)
3528   {
3529     viewport.autoCalculateConsensus = autoCalculate.isSelected();
3530     if (viewport.autoCalculateConsensus)
3531     {
3532       viewport.firePropertyChange("alignment", null,
3533               viewport.getAlignment().getSequences());
3534     }
3535   }
3536
3537   @Override
3538   public void sortByTreeOption_actionPerformed(ActionEvent e)
3539   {
3540     viewport.sortByTree = sortByTree.isSelected();
3541   }
3542
3543   @Override
3544   protected void listenToViewSelections_actionPerformed(ActionEvent e)
3545   {
3546     viewport.followSelection = listenToViewSelections.isSelected();
3547   }
3548
3549   /**
3550    * Constructs a tree panel and adds it to the desktop
3551    *
3552    * @param type
3553    *          tree type (NJ or AV)
3554    * @param modelName
3555    *          name of score model used to compute the tree
3556    * @param options
3557    *          parameters for the distance or similarity calculation
3558    */
3559   void newTreePanel(String type, String modelName,
3560           SimilarityParamsI options)
3561   {
3562     String frameTitle = "";
3563     TreePanel tp;
3564
3565     boolean onSelection = false;
3566     if (viewport.getSelectionGroup() != null
3567             && viewport.getSelectionGroup().getSize() > 0)
3568     {
3569       SequenceGroup sg = viewport.getSelectionGroup();
3570
3571       /* Decide if the selection is a column region */
3572       for (SequenceI _s : sg.getSequences())
3573       {
3574         if (_s.getLength() < sg.getEndRes())
3575         {
3576           JvOptionPane.showMessageDialog(Desktop.desktop,
3577                   MessageManager.getString(
3578                           "label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3579                   MessageManager.getString(
3580                           "label.sequences_selection_not_aligned"),
3581                   JvOptionPane.WARNING_MESSAGE);
3582
3583           return;
3584         }
3585       }
3586       onSelection = true;
3587     }
3588     else
3589     {
3590       if (viewport.getAlignment().getHeight() < 2)
3591       {
3592         return;
3593       }
3594     }
3595
3596     tp = new TreePanel(alignPanel, type, modelName, options);
3597     frameTitle = tp.getPanelTitle() + (onSelection ? " on region" : "");
3598
3599     frameTitle += " from ";
3600
3601     if (viewport.viewName != null)
3602     {
3603       frameTitle += viewport.viewName + " of ";
3604     }
3605
3606     frameTitle += this.title;
3607
3608     Desktop.addInternalFrame(tp, frameTitle, 600, 500);
3609   }
3610
3611   /**
3612    * DOCUMENT ME!
3613    *
3614    * @param title
3615    *          DOCUMENT ME!
3616    * @param order
3617    *          DOCUMENT ME!
3618    */
3619   public void addSortByOrderMenuItem(String title,
3620           final AlignmentOrder order)
3621   {
3622     final JMenuItem item = new JMenuItem(MessageManager
3623             .formatMessage("action.by_title_param", new Object[]
3624             { title }));
3625     sort.add(item);
3626     item.addActionListener(new java.awt.event.ActionListener()
3627     {
3628       @Override
3629       public void actionPerformed(ActionEvent e)
3630       {
3631         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3632
3633         // TODO: JBPNote - have to map order entries to curent SequenceI
3634         // pointers
3635         AlignmentSorter.sortBy(viewport.getAlignment(), order);
3636
3637         addHistoryItem(new OrderCommand(order.getName(), oldOrder,
3638                 viewport.getAlignment()));
3639
3640         alignPanel.paintAlignment(true, false);
3641       }
3642     });
3643   }
3644
3645   /**
3646    * Add a new sort by annotation score menu item
3647    *
3648    * @param sort
3649    *          the menu to add the option to
3650    * @param scoreLabel
3651    *          the label used to retrieve scores for each sequence on the
3652    *          alignment
3653    */
3654   public void addSortByAnnotScoreMenuItem(JMenu sort,
3655           final String scoreLabel)
3656   {
3657     final JMenuItem item = new JMenuItem(scoreLabel);
3658     sort.add(item);
3659     item.addActionListener(new java.awt.event.ActionListener()
3660     {
3661       @Override
3662       public void actionPerformed(ActionEvent e)
3663       {
3664         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3665         AlignmentSorter.sortByAnnotationScore(scoreLabel,
3666                 viewport.getAlignment());// ,viewport.getSelectionGroup());
3667         addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3668                 viewport.getAlignment()));
3669         alignPanel.paintAlignment(true, false);
3670       }
3671     });
3672   }
3673
3674   /**
3675    * last hash for alignment's annotation array - used to minimise cost of
3676    * rebuild.
3677    */
3678   protected int _annotationScoreVectorHash;
3679
3680   /**
3681    * search the alignment and rebuild the sort by annotation score submenu the
3682    * last alignment annotation vector hash is stored to minimize cost of
3683    * rebuilding in subsequence calls.
3684    *
3685    */
3686   @Override
3687   public void buildSortByAnnotationScoresMenu()
3688   {
3689     if (viewport.getAlignment().getAlignmentAnnotation() == null)
3690     {
3691       return;
3692     }
3693
3694     if (viewport.getAlignment().getAlignmentAnnotation()
3695             .hashCode() != _annotationScoreVectorHash)
3696     {
3697       sortByAnnotScore.removeAll();
3698       // almost certainly a quicker way to do this - but we keep it simple
3699       Hashtable scoreSorts = new Hashtable();
3700       AlignmentAnnotation aann[];
3701       for (SequenceI sqa : viewport.getAlignment().getSequences())
3702       {
3703         aann = sqa.getAnnotation();
3704         for (int i = 0; aann != null && i < aann.length; i++)
3705         {
3706           if (aann[i].hasScore() && aann[i].sequenceRef != null)
3707           {
3708             scoreSorts.put(aann[i].label, aann[i].label);
3709           }
3710         }
3711       }
3712       Enumeration labels = scoreSorts.keys();
3713       while (labels.hasMoreElements())
3714       {
3715         addSortByAnnotScoreMenuItem(sortByAnnotScore,
3716                 (String) labels.nextElement());
3717       }
3718       sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3719       scoreSorts.clear();
3720
3721       _annotationScoreVectorHash = viewport.getAlignment()
3722               .getAlignmentAnnotation().hashCode();
3723     }
3724   }
3725
3726   /**
3727    * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3728    * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3729    * call. Listeners are added to remove the menu item when the treePanel is
3730    * closed, and adjust the tree leaf to sequence mapping when the alignment is
3731    * modified.
3732    */
3733   @Override
3734   public void buildTreeSortMenu()
3735   {
3736     sortByTreeMenu.removeAll();
3737
3738     List<Component> comps = PaintRefresher.components
3739             .get(viewport.getSequenceSetId());
3740     List<TreePanel> treePanels = new ArrayList<>();
3741     for (Component comp : comps)
3742     {
3743       if (comp instanceof TreePanel)
3744       {
3745         treePanels.add((TreePanel) comp);
3746       }
3747     }
3748
3749     if (treePanels.size() < 1)
3750     {
3751       sortByTreeMenu.setVisible(false);
3752       return;
3753     }
3754
3755     sortByTreeMenu.setVisible(true);
3756
3757     for (final TreePanel tp : treePanels)
3758     {
3759       final JMenuItem item = new JMenuItem(tp.getTitle());
3760       item.addActionListener(new java.awt.event.ActionListener()
3761       {
3762         @Override
3763         public void actionPerformed(ActionEvent e)
3764         {
3765           tp.sortByTree_actionPerformed();
3766           addHistoryItem(tp.sortAlignmentIn(alignPanel));
3767
3768         }
3769       });
3770
3771       sortByTreeMenu.add(item);
3772     }
3773   }
3774
3775   public boolean sortBy(AlignmentOrder alorder, String undoname)
3776   {
3777     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3778     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
3779     if (undoname != null)
3780     {
3781       addHistoryItem(new OrderCommand(undoname, oldOrder,
3782               viewport.getAlignment()));
3783     }
3784     alignPanel.paintAlignment(true, false);
3785     return true;
3786   }
3787
3788   /**
3789    * Work out whether the whole set of sequences or just the selected set will
3790    * be submitted for multiple alignment.
3791    *
3792    */
3793   public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3794   {
3795     // Now, check we have enough sequences
3796     AlignmentView msa = null;
3797
3798     if ((viewport.getSelectionGroup() != null)
3799             && (viewport.getSelectionGroup().getSize() > 1))
3800     {
3801       // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
3802       // some common interface!
3803       /*
3804        * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
3805        * SequenceI[sz = seqs.getSize(false)];
3806        *
3807        * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
3808        * seqs.getSequenceAt(i); }
3809        */
3810       msa = viewport.getAlignmentView(true);
3811     }
3812     else if (viewport.getSelectionGroup() != null
3813             && viewport.getSelectionGroup().getSize() == 1)
3814     {
3815       int option = JvOptionPane.showConfirmDialog(this,
3816               MessageManager.getString("warn.oneseq_msainput_selection"),
3817               MessageManager.getString("label.invalid_selection"),
3818               JvOptionPane.OK_CANCEL_OPTION);
3819       if (option == JvOptionPane.OK_OPTION)
3820       {
3821         msa = viewport.getAlignmentView(false);
3822       }
3823     }
3824     else
3825     {
3826       msa = viewport.getAlignmentView(false);
3827     }
3828     return msa;
3829   }
3830
3831   /**
3832    * Decides what is submitted to a secondary structure prediction service: the
3833    * first sequence in the alignment, or in the current selection, or, if the
3834    * alignment is 'aligned' (ie padded with gaps), then the currently selected
3835    * region or the whole alignment. (where the first sequence in the set is the
3836    * one that the prediction will be for).
3837    */
3838   public AlignmentView gatherSeqOrMsaForSecStrPrediction()
3839   {
3840     AlignmentView seqs = null;
3841
3842     if ((viewport.getSelectionGroup() != null)
3843             && (viewport.getSelectionGroup().getSize() > 0))
3844     {
3845       seqs = viewport.getAlignmentView(true);
3846     }
3847     else
3848     {
3849       seqs = viewport.getAlignmentView(false);
3850     }
3851     // limit sequences - JBPNote in future - could spawn multiple prediction
3852     // jobs
3853     // TODO: viewport.getAlignment().isAligned is a global state - the local
3854     // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
3855     if (!viewport.getAlignment().isAligned(false))
3856     {
3857       seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
3858       // TODO: if seqs.getSequences().length>1 then should really have warned
3859       // user!
3860
3861     }
3862     return seqs;
3863   }
3864
3865   /**
3866    * DOCUMENT ME!
3867    *
3868    * @param e
3869    *          DOCUMENT ME!
3870    */
3871   @Override
3872   protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
3873   {
3874     // Pick the tree file
3875     JalviewFileChooser chooser = new JalviewFileChooser(
3876             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
3877     chooser.setFileView(new JalviewFileView());
3878     chooser.setDialogTitle(
3879             MessageManager.getString("label.select_newick_like_tree_file"));
3880     chooser.setToolTipText(
3881             MessageManager.getString("label.load_tree_file"));
3882
3883     int value = chooser.showOpenDialog(null);
3884
3885     if (value == JalviewFileChooser.APPROVE_OPTION)
3886     {
3887       String filePath = chooser.getSelectedFile().getPath();
3888       Cache.setProperty("LAST_DIRECTORY", filePath);
3889       NewickFile fin = null;
3890       try
3891       {
3892         fin = new NewickFile(filePath, DataSourceType.FILE);
3893         viewport.setCurrentTree(showNewickTree(fin, filePath).getTree());
3894       } catch (Exception ex)
3895       {
3896         JvOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
3897                 MessageManager.getString("label.problem_reading_tree_file"),
3898                 JvOptionPane.WARNING_MESSAGE);
3899         ex.printStackTrace();
3900       }
3901       if (fin != null && fin.hasWarningMessage())
3902       {
3903         JvOptionPane.showMessageDialog(Desktop.desktop,
3904                 fin.getWarningMessage(),
3905                 MessageManager
3906                         .getString("label.possible_problem_with_tree_file"),
3907                 JvOptionPane.WARNING_MESSAGE);
3908       }
3909     }
3910   }
3911
3912   public TreePanel showNewickTree(NewickFile nf, String treeTitle)
3913   {
3914     return showNewickTree(nf, treeTitle, 600, 500, 4, 5);
3915   }
3916
3917   public TreePanel showNewickTree(NewickFile nf, String treeTitle, int w,
3918           int h, int x, int y)
3919   {
3920     return showNewickTree(nf, treeTitle, null, w, h, x, y);
3921   }
3922
3923   /**
3924    * Add a treeviewer for the tree extracted from a Newick file object to the
3925    * current alignment view
3926    *
3927    * @param nf
3928    *          the tree
3929    * @param title
3930    *          tree viewer title
3931    * @param input
3932    *          Associated alignment input data (or null)
3933    * @param w
3934    *          width
3935    * @param h
3936    *          height
3937    * @param x
3938    *          position
3939    * @param y
3940    *          position
3941    * @return TreePanel handle
3942    */
3943   public TreePanel showNewickTree(NewickFile nf, String treeTitle,
3944           AlignmentView input, int w, int h, int x, int y)
3945   {
3946     TreePanel tp = null;
3947
3948     try
3949     {
3950       nf.parse();
3951
3952       if (nf.getTree() != null)
3953       {
3954         tp = new TreePanel(alignPanel, nf, treeTitle, input);
3955
3956         tp.setSize(w, h);
3957
3958         if (x > 0 && y > 0)
3959         {
3960           tp.setLocation(x, y);
3961         }
3962
3963         Desktop.addInternalFrame(tp, treeTitle, w, h);
3964       }
3965     } catch (Exception ex)
3966     {
3967       ex.printStackTrace();
3968     }
3969
3970     return tp;
3971   }
3972
3973   private boolean buildingMenu = false;
3974
3975   /**
3976    * Generates menu items and listener event actions for web service clients
3977    *
3978    */
3979   public void BuildWebServiceMenu()
3980   {
3981     while (buildingMenu)
3982     {
3983       try
3984       {
3985         System.err.println("Waiting for building menu to finish.");
3986         Thread.sleep(10);
3987       } catch (Exception e)
3988       {
3989       }
3990     }
3991     final AlignFrame me = this;
3992     buildingMenu = true;
3993     new Thread(new Runnable()
3994     {
3995       @Override
3996       public void run()
3997       {
3998         final List<JMenuItem> legacyItems = new ArrayList<>();
3999         try
4000         {
4001           // System.err.println("Building ws menu again "
4002           // + Thread.currentThread());
4003           // TODO: add support for context dependent disabling of services based
4004           // on
4005           // alignment and current selection
4006           // TODO: add additional serviceHandle parameter to specify abstract
4007           // handler
4008           // class independently of AbstractName
4009           // TODO: add in rediscovery GUI function to restart discoverer
4010           // TODO: group services by location as well as function and/or
4011           // introduce
4012           // object broker mechanism.
4013           final Vector<JMenu> wsmenu = new Vector<>();
4014           final IProgressIndicator af = me;
4015
4016           /*
4017            * do not i18n these strings - they are hard-coded in class
4018            * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4019            * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4020            */
4021           final JMenu msawsmenu = new JMenu("Alignment");
4022           final JMenu secstrmenu = new JMenu(
4023                   "Secondary Structure Prediction");
4024           final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4025           final JMenu analymenu = new JMenu("Analysis");
4026           final JMenu dismenu = new JMenu("Protein Disorder");
4027           // JAL-940 - only show secondary structure prediction services from
4028           // the legacy server
4029           if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4030               // &&
4031           Discoverer.services != null && (Discoverer.services.size() > 0))
4032           {
4033             // TODO: refactor to allow list of AbstractName/Handler bindings to
4034             // be
4035             // stored or retrieved from elsewhere
4036             // No MSAWS used any more:
4037             // Vector msaws = null; // (Vector)
4038             // Discoverer.services.get("MsaWS");
4039             Vector secstrpr = (Vector) Discoverer.services
4040                     .get("SecStrPred");
4041             if (secstrpr != null)
4042             {
4043               // Add any secondary structure prediction services
4044               for (int i = 0, j = secstrpr.size(); i < j; i++)
4045               {
4046                 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4047                         .get(i);
4048                 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4049                         .getServiceClient(sh);
4050                 int p = secstrmenu.getItemCount();
4051                 impl.attachWSMenuEntry(secstrmenu, me);
4052                 int q = secstrmenu.getItemCount();
4053                 for (int litm = p; litm < q; litm++)
4054                 {
4055                   legacyItems.add(secstrmenu.getItem(litm));
4056                 }
4057               }
4058             }
4059           }
4060
4061           // Add all submenus in the order they should appear on the web
4062           // services menu
4063           wsmenu.add(msawsmenu);
4064           wsmenu.add(secstrmenu);
4065           wsmenu.add(dismenu);
4066           wsmenu.add(analymenu);
4067           // No search services yet
4068           // wsmenu.add(seqsrchmenu);
4069
4070           javax.swing.SwingUtilities.invokeLater(new Runnable()
4071           {
4072             @Override
4073             public void run()
4074             {
4075               try
4076               {
4077                 webService.removeAll();
4078                 // first, add discovered services onto the webservices menu
4079                 if (wsmenu.size() > 0)
4080                 {
4081                   for (int i = 0, j = wsmenu.size(); i < j; i++)
4082                   {
4083                     webService.add(wsmenu.get(i));
4084                   }
4085                 }
4086                 else
4087                 {
4088                   webService.add(me.webServiceNoServices);
4089                 }
4090                 // TODO: move into separate menu builder class.
4091                 boolean new_sspred = false;
4092                 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4093                 {
4094                   Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4095                   if (jws2servs != null)
4096                   {
4097                     if (jws2servs.hasServices())
4098                     {
4099                       jws2servs.attachWSMenuEntry(webService, me);
4100                       for (Jws2Instance sv : jws2servs.getServices())
4101                       {
4102                         if (sv.description.toLowerCase().contains("jpred"))
4103                         {
4104                           for (JMenuItem jmi : legacyItems)
4105                           {
4106                             jmi.setVisible(false);
4107                           }
4108                         }
4109                       }
4110
4111                     }
4112                     if (jws2servs.isRunning())
4113                     {
4114                       JMenuItem tm = new JMenuItem(
4115                               "Still discovering JABA Services");
4116                       tm.setEnabled(false);
4117                       webService.add(tm);
4118                     }
4119                   }
4120                 }
4121                 build_urlServiceMenu(me.webService);
4122                 build_fetchdbmenu(webService);
4123                 for (JMenu item : wsmenu)
4124                 {
4125                   if (item.getItemCount() == 0)
4126                   {
4127                     item.setEnabled(false);
4128                   }
4129                   else
4130                   {
4131                     item.setEnabled(true);
4132                   }
4133                 }
4134               } catch (Exception e)
4135               {
4136                 Cache.log.debug(
4137                         "Exception during web service menu building process.",
4138                         e);
4139               }
4140             }
4141           });
4142         } catch (Exception e)
4143         {
4144         }
4145         buildingMenu = false;
4146       }
4147     }).start();
4148
4149   }
4150
4151   /**
4152    * construct any groupURL type service menu entries.
4153    *
4154    * @param webService
4155    */
4156   private void build_urlServiceMenu(JMenu webService)
4157   {
4158     // TODO: remove this code when 2.7 is released
4159     // DEBUG - alignmentView
4160     /*
4161      * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4162      * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4163      *
4164      * @Override public void actionPerformed(ActionEvent e) {
4165      * jalview.datamodel.AlignmentView
4166      * .testSelectionViews(af.viewport.getAlignment(),
4167      * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4168      *
4169      * }); webService.add(testAlView);
4170      */
4171     // TODO: refactor to RestClient discoverer and merge menu entries for
4172     // rest-style services with other types of analysis/calculation service
4173     // SHmmr test client - still being implemented.
4174     // DEBUG - alignmentView
4175
4176     for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4177             .getRestClients())
4178     {
4179       client.attachWSMenuEntry(
4180               JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4181               this);
4182     }
4183   }
4184
4185   /**
4186    * Searches the alignment sequences for xRefs and builds the Show
4187    * Cross-References menu (formerly called Show Products), with database
4188    * sources for which cross-references are found (protein sources for a
4189    * nucleotide alignment and vice versa)
4190    *
4191    * @return true if Show Cross-references menu should be enabled
4192    */
4193   public boolean canShowProducts()
4194   {
4195     SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4196     AlignmentI dataset = viewport.getAlignment().getDataset();
4197
4198     showProducts.removeAll();
4199     final boolean dna = viewport.getAlignment().isNucleotide();
4200
4201     if (seqs == null || seqs.length == 0)
4202     {
4203       // nothing to see here.
4204       return false;
4205     }
4206
4207     boolean showp = false;
4208     try
4209     {
4210       List<String> ptypes = new CrossRef(seqs, dataset)
4211               .findXrefSourcesForSequences(dna);
4212
4213       for (final String source : ptypes)
4214       {
4215         showp = true;
4216         final AlignFrame af = this;
4217         JMenuItem xtype = new JMenuItem(source);
4218         xtype.addActionListener(new ActionListener()
4219         {
4220           @Override
4221           public void actionPerformed(ActionEvent e)
4222           {
4223             showProductsFor(af.viewport.getSequenceSelection(), dna,
4224                     source);
4225           }
4226         });
4227         showProducts.add(xtype);
4228       }
4229       showProducts.setVisible(showp);
4230       showProducts.setEnabled(showp);
4231     } catch (Exception e)
4232     {
4233       Cache.log.warn(
4234               "canShowProducts threw an exception - please report to help@jalview.org",
4235               e);
4236       return false;
4237     }
4238     return showp;
4239   }
4240
4241   /**
4242    * Finds and displays cross-references for the selected sequences (protein
4243    * products for nucleotide sequences, dna coding sequences for peptides).
4244    *
4245    * @param sel
4246    *          the sequences to show cross-references for
4247    * @param dna
4248    *          true if from a nucleotide alignment (so showing proteins)
4249    * @param source
4250    *          the database to show cross-references for
4251    */
4252   protected void showProductsFor(final SequenceI[] sel, final boolean _odna,
4253           final String source)
4254   {
4255     new Thread(CrossRefAction.showProductsFor(sel, _odna, source, this))
4256             .start();
4257   }
4258
4259   /**
4260    * Construct and display a new frame containing the translation of this
4261    * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4262    */
4263   @Override
4264   public void showTranslation_actionPerformed(ActionEvent e)
4265   {
4266     AlignmentI al = null;
4267     try
4268     {
4269       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4270
4271       al = dna.translateCdna();
4272     } catch (Exception ex)
4273     {
4274       jalview.bin.Cache.log.error(
4275               "Exception during translation. Please report this !", ex);
4276       final String msg = MessageManager.getString(
4277               "label.error_when_translating_sequences_submit_bug_report");
4278       final String errorTitle = MessageManager
4279               .getString("label.implementation_error")
4280               + MessageManager.getString("label.translation_failed");
4281       JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4282               JvOptionPane.ERROR_MESSAGE);
4283       return;
4284     }
4285     if (al == null || al.getHeight() == 0)
4286     {
4287       final String msg = MessageManager.getString(
4288               "label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4289       final String errorTitle = MessageManager
4290               .getString("label.translation_failed");
4291       JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4292               JvOptionPane.WARNING_MESSAGE);
4293     }
4294     else
4295     {
4296       AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4297       af.setFileFormat(this.currentFileFormat);
4298       final String newTitle = MessageManager
4299               .formatMessage("label.translation_of_params", new Object[]
4300               { this.getTitle() });
4301       af.setTitle(newTitle);
4302       if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4303       {
4304         final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4305         viewport.openSplitFrame(af, new Alignment(seqs));
4306       }
4307       else
4308       {
4309         Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4310                 DEFAULT_HEIGHT);
4311       }
4312     }
4313   }
4314
4315   /**
4316    * Set the file format
4317    *
4318    * @param format
4319    */
4320   public void setFileFormat(FileFormatI format)
4321   {
4322     this.currentFileFormat = format;
4323   }
4324
4325   /**
4326    * Try to load a features file onto the alignment.
4327    *
4328    * @param file
4329    *          contents or path to retrieve file
4330    * @param sourceType
4331    *          access mode of file (see jalview.io.AlignFile)
4332    * @return true if features file was parsed correctly.
4333    */
4334   public boolean parseFeaturesFile(String file, DataSourceType sourceType)
4335   {
4336     return avc.parseFeaturesFile(file, sourceType,
4337             Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4338
4339   }
4340
4341   @Override
4342   public void refreshFeatureUI(boolean enableIfNecessary)
4343   {
4344     // note - currently this is only still here rather than in the controller
4345     // because of the featureSettings hard reference that is yet to be
4346     // abstracted
4347     if (enableIfNecessary)
4348     {
4349       viewport.setShowSequenceFeatures(true);
4350       showSeqFeatures.setSelected(true);
4351     }
4352
4353   }
4354
4355   @Override
4356   public void dragEnter(DropTargetDragEvent evt)
4357   {
4358   }
4359
4360   @Override
4361   public void dragExit(DropTargetEvent evt)
4362   {
4363   }
4364
4365   @Override
4366   public void dragOver(DropTargetDragEvent evt)
4367   {
4368   }
4369
4370   @Override
4371   public void dropActionChanged(DropTargetDragEvent evt)
4372   {
4373   }
4374
4375   @Override
4376   public void drop(DropTargetDropEvent evt)
4377   {
4378     // JAL-1552 - acceptDrop required before getTransferable call for
4379     // Java's Transferable for native dnd
4380     evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4381     Transferable t = evt.getTransferable();
4382     final AlignFrame thisaf = this;
4383     final List<String> files = new ArrayList<>();
4384     List<DataSourceType> protocols = new ArrayList<>();
4385
4386     try
4387     {
4388       Desktop.transferFromDropTarget(files, protocols, evt, t);
4389     } catch (Exception e)
4390     {
4391       e.printStackTrace();
4392     }
4393     if (files != null)
4394     {
4395       new Thread(new Runnable()
4396       {
4397         @Override
4398         public void run()
4399         {
4400           try
4401           {
4402             // check to see if any of these files have names matching sequences
4403             // in
4404             // the alignment
4405             SequenceIdMatcher idm = new SequenceIdMatcher(
4406                     viewport.getAlignment().getSequencesArray());
4407             /**
4408              * Object[] { String,SequenceI}
4409              */
4410             ArrayList<Object[]> filesmatched = new ArrayList<>();
4411             ArrayList<String> filesnotmatched = new ArrayList<>();
4412             for (int i = 0; i < files.size(); i++)
4413             {
4414               String file = files.get(i).toString();
4415               String pdbfn = "";
4416               DataSourceType protocol = FormatAdapter.checkProtocol(file);
4417               if (protocol == DataSourceType.FILE)
4418               {
4419                 File fl = new File(file);
4420                 pdbfn = fl.getName();
4421               }
4422               else if (protocol == DataSourceType.URL)
4423               {
4424                 URL url = new URL(file);
4425                 pdbfn = url.getFile();
4426               }
4427               if (pdbfn.length() > 0)
4428               {
4429                 // attempt to find a match in the alignment
4430                 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4431                 int l = 0, c = pdbfn.indexOf(".");
4432                 while (mtch == null && c != -1)
4433                 {
4434                   do
4435                   {
4436                     l = c;
4437                   } while ((c = pdbfn.indexOf(".", l)) > l);
4438                   if (l > -1)
4439                   {
4440                     pdbfn = pdbfn.substring(0, l);
4441                   }
4442                   mtch = idm.findAllIdMatches(pdbfn);
4443                 }
4444                 if (mtch != null)
4445                 {
4446                   FileFormatI type = null;
4447                   try
4448                   {
4449                     type = new IdentifyFile().identify(file, protocol);
4450                   } catch (Exception ex)
4451                   {
4452                     type = null;
4453                   }
4454                   if (type != null && type.isStructureFile())
4455                   {
4456                     filesmatched.add(new Object[] { file, protocol, mtch });
4457                     continue;
4458                   }
4459                 }
4460                 // File wasn't named like one of the sequences or wasn't a PDB
4461                 // file.
4462                 filesnotmatched.add(file);
4463               }
4464             }
4465             int assocfiles = 0;
4466             if (filesmatched.size() > 0)
4467             {
4468               if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
4469                       || JvOptionPane.showConfirmDialog(thisaf,
4470                               MessageManager.formatMessage(
4471                                       "label.automatically_associate_structure_files_with_sequences_same_name",
4472                                       new Object[]
4473                                       { Integer.valueOf(filesmatched.size())
4474                                               .toString() }),
4475                               MessageManager.getString(
4476                                       "label.automatically_associate_structure_files_by_name"),
4477                               JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION)
4478
4479               {
4480                 for (Object[] fm : filesmatched)
4481                 {
4482                   // try and associate
4483                   // TODO: may want to set a standard ID naming formalism for
4484                   // associating PDB files which have no IDs.
4485                   for (SequenceI toassoc : (SequenceI[]) fm[2])
4486                   {
4487                     PDBEntry pe = new AssociatePdbFileWithSeq()
4488                             .associatePdbWithSeq((String) fm[0],
4489                                     (DataSourceType) fm[1], toassoc, false,
4490                                     Desktop.instance);
4491                     if (pe != null)
4492                     {
4493                       System.err.println("Associated file : "
4494                               + ((String) fm[0]) + " with "
4495                               + toassoc.getDisplayId(true));
4496                       assocfiles++;
4497                     }
4498                   }
4499                   // TODO: do we need to update overview ? only if features are
4500                   // shown I guess
4501                   alignPanel.paintAlignment(true, false);
4502                 }
4503               }
4504             }
4505             if (filesnotmatched.size() > 0)
4506             {
4507               if (assocfiles > 0 && (Cache.getDefault(
4508                       "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false)
4509                       || JvOptionPane.showConfirmDialog(thisaf,
4510                               "<html>" + MessageManager.formatMessage(
4511                                       "label.ignore_unmatched_dropped_files_info",
4512                                       new Object[]
4513                                       { Integer.valueOf(
4514                                               filesnotmatched.size())
4515                                               .toString() })
4516                                       + "</html>",
4517                               MessageManager.getString(
4518                                       "label.ignore_unmatched_dropped_files"),
4519                               JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
4520               {
4521                 return;
4522               }
4523               for (String fn : filesnotmatched)
4524               {
4525                 loadJalviewDataFile(fn, null, null, null);
4526               }
4527
4528             }
4529           } catch (Exception ex)
4530           {
4531             ex.printStackTrace();
4532           }
4533         }
4534       }).start();
4535     }
4536   }
4537
4538   /**
4539    * Attempt to load a "dropped" file or URL string, by testing in turn for
4540    * <ul>
4541    * <li>an Annotation file</li>
4542    * <li>a JNet file</li>
4543    * <li>a features file</li>
4544    * <li>else try to interpret as an alignment file</li>
4545    * </ul>
4546    *
4547    * @param file
4548    *          either a filename or a URL string.
4549    */
4550   public void loadJalviewDataFile(String file, DataSourceType sourceType,
4551           FileFormatI format, SequenceI assocSeq)
4552   {
4553     try
4554     {
4555       if (sourceType == null)
4556       {
4557         sourceType = FormatAdapter.checkProtocol(file);
4558       }
4559       // if the file isn't identified, or not positively identified as some
4560       // other filetype (PFAM is default unidentified alignment file type) then
4561       // try to parse as annotation.
4562       boolean isAnnotation = (format == null
4563               || FileFormat.Pfam.equals(format))
4564                       ? new AnnotationFile().annotateAlignmentView(viewport,
4565                               file, sourceType)
4566                       : false;
4567
4568       if (!isAnnotation)
4569       {
4570         // first see if its a T-COFFEE score file
4571         TCoffeeScoreFile tcf = null;
4572         try
4573         {
4574           tcf = new TCoffeeScoreFile(file, sourceType);
4575           if (tcf.isValid())
4576           {
4577             if (tcf.annotateAlignment(viewport.getAlignment(), true))
4578             {
4579               buildColourMenu();
4580               changeColour(
4581                       new TCoffeeColourScheme(viewport.getAlignment()));
4582               isAnnotation = true;
4583               statusBar.setText(MessageManager.getString(
4584                       "label.successfully_pasted_tcoffee_scores_to_alignment"));
4585             }
4586             else
4587             {
4588               // some problem - if no warning its probable that the ID matching
4589               // process didn't work
4590               JvOptionPane.showMessageDialog(Desktop.desktop,
4591                       tcf.getWarningMessage() == null
4592                               ? MessageManager.getString(
4593                                       "label.check_file_matches_sequence_ids_alignment")
4594                               : tcf.getWarningMessage(),
4595                       MessageManager.getString(
4596                               "label.problem_reading_tcoffee_score_file"),
4597                       JvOptionPane.WARNING_MESSAGE);
4598             }
4599           }
4600           else
4601           {
4602             tcf = null;
4603           }
4604         } catch (Exception x)
4605         {
4606           Cache.log.debug(
4607                   "Exception when processing data source as T-COFFEE score file",
4608                   x);
4609           tcf = null;
4610         }
4611         if (tcf == null)
4612         {
4613           // try to see if its a JNet 'concise' style annotation file *before*
4614           // we
4615           // try to parse it as a features file
4616           if (format == null)
4617           {
4618             format = new IdentifyFile().identify(file, sourceType);
4619           }
4620           if (FileFormat.ScoreMatrix == format)
4621           {
4622             ScoreMatrixFile sm = new ScoreMatrixFile(
4623                     new FileParse(file, sourceType));
4624             sm.parse();
4625             // todo: i18n this message
4626             statusBar.setText(MessageManager.formatMessage(
4627                     "label.successfully_loaded_matrix",
4628                     sm.getMatrixName()));
4629           }
4630           else if (FileFormat.Jnet.equals(format))
4631           {
4632             JPredFile predictions = new JPredFile(file, sourceType);
4633             new JnetAnnotationMaker();
4634             JnetAnnotationMaker.add_annotation(predictions,
4635                     viewport.getAlignment(), 0, false);
4636             SequenceI repseq = viewport.getAlignment().getSequenceAt(0);
4637             viewport.getAlignment().setSeqrep(repseq);
4638             HiddenColumns cs = new HiddenColumns();
4639             cs.hideInsertionsFor(repseq);
4640             viewport.getAlignment().setHiddenColumns(cs);
4641             isAnnotation = true;
4642           }
4643           // else if (IdentifyFile.FeaturesFile.equals(format))
4644           else if (FileFormat.Features.equals(format))
4645           {
4646             if (parseFeaturesFile(file, sourceType))
4647             {
4648               alignPanel.paintAlignment(true, true);
4649             }
4650           }
4651           else
4652           {
4653             new FileLoader().LoadFile(viewport, file, sourceType, format);
4654           }
4655         }
4656       }
4657       if (isAnnotation)
4658       {
4659
4660         alignPanel.adjustAnnotationHeight();
4661         viewport.updateSequenceIdColours();
4662         buildSortByAnnotationScoresMenu();
4663         alignPanel.paintAlignment(true, true);
4664       }
4665     } catch (Exception ex)
4666     {
4667       ex.printStackTrace();
4668     } catch (OutOfMemoryError oom)
4669     {
4670       try
4671       {
4672         System.gc();
4673       } catch (Exception x)
4674       {
4675       }
4676       new OOMWarning(
4677               "loading data "
4678                       + (sourceType != null
4679                               ? (sourceType == DataSourceType.PASTE
4680                                       ? "from clipboard."
4681                                       : "using " + sourceType + " from "
4682                                               + file)
4683                               : ".")
4684                       + (format != null
4685                               ? "(parsing as '" + format + "' file)"
4686                               : ""),
4687               oom, Desktop.desktop);
4688     }
4689   }
4690
4691   /**
4692    * Method invoked by the ChangeListener on the tabbed pane, in other words
4693    * when a different tabbed pane is selected by the user or programmatically.
4694    */
4695   @Override
4696   public void tabSelectionChanged(int index)
4697   {
4698     if (index > -1)
4699     {
4700       alignPanel = alignPanels.get(index);
4701       viewport = alignPanel.av;
4702       avc.setViewportAndAlignmentPanel(viewport, alignPanel);
4703       setMenusFromViewport(viewport);
4704     }
4705
4706     /*
4707      * 'focus' any colour slider that is open to the selected viewport
4708      */
4709     if (viewport.getConservationSelected())
4710     {
4711       SliderPanel.setConservationSlider(alignPanel,
4712               viewport.getResidueShading(), alignPanel.getViewName());
4713     }
4714     else
4715     {
4716       SliderPanel.hideConservationSlider();
4717     }
4718     if (viewport.getAbovePIDThreshold())
4719     {
4720       SliderPanel.setPIDSliderSource(alignPanel,
4721               viewport.getResidueShading(), alignPanel.getViewName());
4722     }
4723     else
4724     {
4725       SliderPanel.hidePIDSlider();
4726     }
4727
4728     /*
4729      * If there is a frame linked to this one in a SplitPane, switch it to the
4730      * same view tab index. No infinite recursion of calls should happen, since
4731      * tabSelectionChanged() should not get invoked on setting the selected
4732      * index to an unchanged value. Guard against setting an invalid index
4733      * before the new view peer tab has been created.
4734      */
4735     final AlignViewportI peer = viewport.getCodingComplement();
4736     if (peer != null)
4737     {
4738       AlignFrame linkedAlignFrame = ((AlignViewport) peer)
4739               .getAlignPanel().alignFrame;
4740       if (linkedAlignFrame.tabbedPane.getTabCount() > index)
4741       {
4742         linkedAlignFrame.tabbedPane.setSelectedIndex(index);
4743       }
4744     }
4745   }
4746
4747   /**
4748    * On right mouse click on view tab, prompt for and set new view name.
4749    */
4750   @Override
4751   public void tabbedPane_mousePressed(MouseEvent e)
4752   {
4753     if (e.isPopupTrigger())
4754     {
4755       String msg = MessageManager.getString("label.enter_view_name");
4756       String reply = JvOptionPane.showInternalInputDialog(this, msg, msg,
4757               JvOptionPane.QUESTION_MESSAGE);
4758
4759       if (reply != null)
4760       {
4761         viewport.viewName = reply;
4762         // TODO warn if reply is in getExistingViewNames()?
4763         tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
4764       }
4765     }
4766   }
4767
4768   public AlignViewport getCurrentView()
4769   {
4770     return viewport;
4771   }
4772
4773   /**
4774    * Open the dialog for regex description parsing.
4775    */
4776   @Override
4777   protected void extractScores_actionPerformed(ActionEvent e)
4778   {
4779     ParseProperties pp = new jalview.analysis.ParseProperties(
4780             viewport.getAlignment());
4781     // TODO: verify regex and introduce GUI dialog for version 2.5
4782     // if (pp.getScoresFromDescription("col", "score column ",
4783     // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
4784     // true)>0)
4785     if (pp.getScoresFromDescription("description column",
4786             "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
4787     {
4788       buildSortByAnnotationScoresMenu();
4789     }
4790   }
4791
4792   /*
4793    * (non-Javadoc)
4794    *
4795    * @see
4796    * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
4797    * )
4798    */
4799   @Override
4800   protected void showDbRefs_actionPerformed(ActionEvent e)
4801   {
4802     viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
4803   }
4804
4805   /*
4806    * (non-Javadoc)
4807    *
4808    * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
4809    * ActionEvent)
4810    */
4811   @Override
4812   protected void showNpFeats_actionPerformed(ActionEvent e)
4813   {
4814     viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
4815   }
4816
4817   /**
4818    * find the viewport amongst the tabs in this alignment frame and close that
4819    * tab
4820    *
4821    * @param av
4822    */
4823   public boolean closeView(AlignViewportI av)
4824   {
4825     if (viewport == av)
4826     {
4827       this.closeMenuItem_actionPerformed(false);
4828       return true;
4829     }
4830     Component[] comp = tabbedPane.getComponents();
4831     for (int i = 0; comp != null && i < comp.length; i++)
4832     {
4833       if (comp[i] instanceof AlignmentPanel)
4834       {
4835         if (((AlignmentPanel) comp[i]).av == av)
4836         {
4837           // close the view.
4838           closeView((AlignmentPanel) comp[i]);
4839           return true;
4840         }
4841       }
4842     }
4843     return false;
4844   }
4845
4846   protected void build_fetchdbmenu(JMenu webService)
4847   {
4848     // Temporary hack - DBRef Fetcher always top level ws entry.
4849     // TODO We probably want to store a sequence database checklist in
4850     // preferences and have checkboxes.. rather than individual sources selected
4851     // here
4852     final JMenu rfetch = new JMenu(
4853             MessageManager.getString("action.fetch_db_references"));
4854     rfetch.setToolTipText(MessageManager.getString(
4855             "label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
4856     webService.add(rfetch);
4857
4858     final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
4859             MessageManager.getString("option.trim_retrieved_seqs"));
4860     trimrs.setToolTipText(
4861             MessageManager.getString("label.trim_retrieved_sequences"));
4862     trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true));
4863     trimrs.addActionListener(new ActionListener()
4864     {
4865       @Override
4866       public void actionPerformed(ActionEvent e)
4867       {
4868         trimrs.setSelected(trimrs.isSelected());
4869         Cache.setProperty("TRIM_FETCHED_DATASET_SEQS",
4870                 Boolean.valueOf(trimrs.isSelected()).toString());
4871       };
4872     });
4873     rfetch.add(trimrs);
4874     JMenuItem fetchr = new JMenuItem(
4875             MessageManager.getString("label.standard_databases"));
4876     fetchr.setToolTipText(
4877             MessageManager.getString("label.fetch_embl_uniprot"));
4878     fetchr.addActionListener(new ActionListener()
4879     {
4880
4881       @Override
4882       public void actionPerformed(ActionEvent e)
4883       {
4884         new Thread(new Runnable()
4885         {
4886           @Override
4887           public void run()
4888           {
4889             boolean isNucleotide = alignPanel.alignFrame.getViewport()
4890                     .getAlignment().isNucleotide();
4891             DBRefFetcher dbRefFetcher = new DBRefFetcher(
4892                     alignPanel.av.getSequenceSelection(),
4893                     alignPanel.alignFrame, null,
4894                     alignPanel.alignFrame.featureSettings, isNucleotide);
4895             dbRefFetcher.addListener(new FetchFinishedListenerI()
4896             {
4897               @Override
4898               public void finished()
4899               {
4900                 AlignFrame.this.setMenusForViewport();
4901               }
4902             });
4903             dbRefFetcher.fetchDBRefs(false);
4904           }
4905         }).start();
4906
4907       }
4908
4909     });
4910     rfetch.add(fetchr);
4911     final AlignFrame me = this;
4912     new Thread(new Runnable()
4913     {
4914       @Override
4915       public void run()
4916       {
4917         final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
4918                 .getSequenceFetcherSingleton(me);
4919         javax.swing.SwingUtilities.invokeLater(new Runnable()
4920         {
4921           @Override
4922           public void run()
4923           {
4924             String[] dbclasses = sf.getOrderedSupportedSources();
4925             // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
4926             // jalview.util.QuickSort.sort(otherdb, otherdb);
4927             List<DbSourceProxy> otherdb;
4928             JMenu dfetch = new JMenu();
4929             JMenu ifetch = new JMenu();
4930             JMenuItem fetchr = null;
4931             int comp = 0, icomp = 0, mcomp = 15;
4932             String mname = null;
4933             int dbi = 0;
4934             for (String dbclass : dbclasses)
4935             {
4936               otherdb = sf.getSourceProxy(dbclass);
4937               // add a single entry for this class, or submenu allowing 'fetch
4938               // all' or pick one
4939               if (otherdb == null || otherdb.size() < 1)
4940               {
4941                 continue;
4942               }
4943               // List<DbSourceProxy> dbs=otherdb;
4944               // otherdb=new ArrayList<DbSourceProxy>();
4945               // for (DbSourceProxy db:dbs)
4946               // {
4947               // if (!db.isA(DBRefSource.ALIGNMENTDB)
4948               // }
4949               if (mname == null)
4950               {
4951                 mname = "From " + dbclass;
4952               }
4953               if (otherdb.size() == 1)
4954               {
4955                 final DbSourceProxy[] dassource = otherdb
4956                         .toArray(new DbSourceProxy[0]);
4957                 DbSourceProxy src = otherdb.get(0);
4958                 fetchr = new JMenuItem(src.getDbSource());
4959                 fetchr.addActionListener(new ActionListener()
4960                 {
4961
4962                   @Override
4963                   public void actionPerformed(ActionEvent e)
4964                   {
4965                     new Thread(new Runnable()
4966                     {
4967
4968                       @Override
4969                       public void run()
4970                       {
4971                         boolean isNucleotide = alignPanel.alignFrame
4972                                 .getViewport().getAlignment()
4973                                 .isNucleotide();
4974                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
4975                                 alignPanel.av.getSequenceSelection(),
4976                                 alignPanel.alignFrame, dassource,
4977                                 alignPanel.alignFrame.featureSettings,
4978                                 isNucleotide);
4979                         dbRefFetcher
4980                                 .addListener(new FetchFinishedListenerI()
4981                                 {
4982                                   @Override
4983                                   public void finished()
4984                                   {
4985                                     AlignFrame.this.setMenusForViewport();
4986                                   }
4987                                 });
4988                         dbRefFetcher.fetchDBRefs(false);
4989                       }
4990                     }).start();
4991                   }
4992
4993                 });
4994                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
4995                         MessageManager.formatMessage(
4996                                 "label.fetch_retrieve_from", new Object[]
4997                                 { src.getDbName() })));
4998                 dfetch.add(fetchr);
4999                 comp++;
5000               }
5001               else
5002               {
5003                 final DbSourceProxy[] dassource = otherdb
5004                         .toArray(new DbSourceProxy[0]);
5005                 // fetch all entry
5006                 DbSourceProxy src = otherdb.get(0);
5007                 fetchr = new JMenuItem(MessageManager
5008                         .formatMessage("label.fetch_all_param", new Object[]
5009                         { src.getDbSource() }));
5010                 fetchr.addActionListener(new ActionListener()
5011                 {
5012                   @Override
5013                   public void actionPerformed(ActionEvent e)
5014                   {
5015                     new Thread(new Runnable()
5016                     {
5017
5018                       @Override
5019                       public void run()
5020                       {
5021                         boolean isNucleotide = alignPanel.alignFrame
5022                                 .getViewport().getAlignment()
5023                                 .isNucleotide();
5024                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5025                                 alignPanel.av.getSequenceSelection(),
5026                                 alignPanel.alignFrame, dassource,
5027                                 alignPanel.alignFrame.featureSettings,
5028                                 isNucleotide);
5029                         dbRefFetcher
5030                                 .addListener(new FetchFinishedListenerI()
5031                                 {
5032                                   @Override
5033                                   public void finished()
5034                                   {
5035                                     AlignFrame.this.setMenusForViewport();
5036                                   }
5037                                 });
5038                         dbRefFetcher.fetchDBRefs(false);
5039                       }
5040                     }).start();
5041                   }
5042                 });
5043
5044                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5045                         MessageManager.formatMessage(
5046                                 "label.fetch_retrieve_from_all_sources",
5047                                 new Object[]
5048                                 { Integer.valueOf(otherdb.size())
5049                                         .toString(),
5050                                     src.getDbSource(), src.getDbName() })));
5051                 dfetch.add(fetchr);
5052                 comp++;
5053                 // and then build the rest of the individual menus
5054                 ifetch = new JMenu(MessageManager.formatMessage(
5055                         "label.source_from_db_source", new Object[]
5056                         { src.getDbSource() }));
5057                 icomp = 0;
5058                 String imname = null;
5059                 int i = 0;
5060                 for (DbSourceProxy sproxy : otherdb)
5061                 {
5062                   String dbname = sproxy.getDbName();
5063                   String sname = dbname.length() > 5
5064                           ? dbname.substring(0, 5) + "..."
5065                           : dbname;
5066                   String msname = dbname.length() > 10
5067                           ? dbname.substring(0, 10) + "..."
5068                           : dbname;
5069                   if (imname == null)
5070                   {
5071                     imname = MessageManager
5072                             .formatMessage("label.from_msname", new Object[]
5073                             { sname });
5074                   }
5075                   fetchr = new JMenuItem(msname);
5076                   final DbSourceProxy[] dassrc = { sproxy };
5077                   fetchr.addActionListener(new ActionListener()
5078                   {
5079
5080                     @Override
5081                     public void actionPerformed(ActionEvent e)
5082                     {
5083                       new Thread(new Runnable()
5084                       {
5085
5086                         @Override
5087                         public void run()
5088                         {
5089                           boolean isNucleotide = alignPanel.alignFrame
5090                                   .getViewport().getAlignment()
5091                                   .isNucleotide();
5092                           DBRefFetcher dbRefFetcher = new DBRefFetcher(
5093                                   alignPanel.av.getSequenceSelection(),
5094                                   alignPanel.alignFrame, dassrc,
5095                                   alignPanel.alignFrame.featureSettings,
5096                                   isNucleotide);
5097                           dbRefFetcher
5098                                   .addListener(new FetchFinishedListenerI()
5099                                   {
5100                                     @Override
5101                                     public void finished()
5102                                     {
5103                                       AlignFrame.this.setMenusForViewport();
5104                                     }
5105                                   });
5106                           dbRefFetcher.fetchDBRefs(false);
5107                         }
5108                       }).start();
5109                     }
5110
5111                   });
5112                   fetchr.setToolTipText(
5113                           "<html>" + MessageManager.formatMessage(
5114                                   "label.fetch_retrieve_from", new Object[]
5115                                   { dbname }));
5116                   ifetch.add(fetchr);
5117                   ++i;
5118                   if (++icomp >= mcomp || i == (otherdb.size()))
5119                   {
5120                     ifetch.setText(MessageManager.formatMessage(
5121                             "label.source_to_target", imname, sname));
5122                     dfetch.add(ifetch);
5123                     ifetch = new JMenu();
5124                     imname = null;
5125                     icomp = 0;
5126                     comp++;
5127                   }
5128                 }
5129               }
5130               ++dbi;
5131               if (comp >= mcomp || dbi >= (dbclasses.length))
5132               {
5133                 dfetch.setText(MessageManager.formatMessage(
5134                         "label.source_to_target", mname, dbclass));
5135                 rfetch.add(dfetch);
5136                 dfetch = new JMenu();
5137                 mname = null;
5138                 comp = 0;
5139               }
5140             }
5141           }
5142         });
5143       }
5144     }).start();
5145
5146   }
5147
5148   /**
5149    * Left justify the whole alignment.
5150    */
5151   @Override
5152   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5153   {
5154     AlignmentI al = viewport.getAlignment();
5155     al.justify(false);
5156     viewport.firePropertyChange("alignment", null, al);
5157   }
5158
5159   /**
5160    * Right justify the whole alignment.
5161    */
5162   @Override
5163   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5164   {
5165     AlignmentI al = viewport.getAlignment();
5166     al.justify(true);
5167     viewport.firePropertyChange("alignment", null, al);
5168   }
5169
5170   @Override
5171   public void setShowSeqFeatures(boolean b)
5172   {
5173     showSeqFeatures.setSelected(b);
5174     viewport.setShowSequenceFeatures(b);
5175   }
5176
5177   /*
5178    * (non-Javadoc)
5179    *
5180    * @see
5181    * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5182    * awt.event.ActionEvent)
5183    */
5184   @Override
5185   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5186   {
5187     viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5188     alignPanel.paintAlignment(false, false);
5189   }
5190
5191   /*
5192    * (non-Javadoc)
5193    *
5194    * @see
5195    * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5196    * .ActionEvent)
5197    */
5198   @Override
5199   protected void showGroupConsensus_actionPerformed(ActionEvent e)
5200   {
5201     viewport.setShowGroupConsensus(showGroupConsensus.getState());
5202     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5203
5204   }
5205
5206   /*
5207    * (non-Javadoc)
5208    *
5209    * @see
5210    * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5211    * .event.ActionEvent)
5212    */
5213   @Override
5214   protected void showGroupConservation_actionPerformed(ActionEvent e)
5215   {
5216     viewport.setShowGroupConservation(showGroupConservation.getState());
5217     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5218   }
5219
5220   /*
5221    * (non-Javadoc)
5222    *
5223    * @see
5224    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5225    * .event.ActionEvent)
5226    */
5227   @Override
5228   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5229   {
5230     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5231     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5232   }
5233
5234   /*
5235    * (non-Javadoc)
5236    *
5237    * @see
5238    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5239    * .event.ActionEvent)
5240    */
5241   @Override
5242   protected void showSequenceLogo_actionPerformed(ActionEvent e)
5243   {
5244     viewport.setShowSequenceLogo(showSequenceLogo.getState());
5245     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5246   }
5247
5248   @Override
5249   protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5250   {
5251     showSequenceLogo.setState(true);
5252     viewport.setShowSequenceLogo(true);
5253     viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5254     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5255   }
5256
5257   @Override
5258   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5259   {
5260     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5261   }
5262
5263   /*
5264    * (non-Javadoc)
5265    *
5266    * @see
5267    * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5268    * .event.ActionEvent)
5269    */
5270   @Override
5271   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5272   {
5273     if (avc.makeGroupsFromSelection())
5274     {
5275       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5276       alignPanel.updateAnnotation();
5277       alignPanel.paintAlignment(true, true);
5278     }
5279   }
5280
5281   public void clearAlignmentSeqRep()
5282   {
5283     // TODO refactor alignmentseqrep to controller
5284     if (viewport.getAlignment().hasSeqrep())
5285     {
5286       viewport.getAlignment().setSeqrep(null);
5287       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5288       alignPanel.updateAnnotation();
5289       alignPanel.paintAlignment(true, true);
5290     }
5291   }
5292
5293   @Override
5294   protected void createGroup_actionPerformed(ActionEvent e)
5295   {
5296     if (avc.createGroup())
5297     {
5298       alignPanel.alignmentChanged();
5299     }
5300   }
5301
5302   @Override
5303   protected void unGroup_actionPerformed(ActionEvent e)
5304   {
5305     if (avc.unGroup())
5306     {
5307       alignPanel.alignmentChanged();
5308     }
5309   }
5310
5311   /**
5312    * make the given alignmentPanel the currently selected tab
5313    *
5314    * @param alignmentPanel
5315    */
5316   public void setDisplayedView(AlignmentPanel alignmentPanel)
5317   {
5318     if (!viewport.getSequenceSetId()
5319             .equals(alignmentPanel.av.getSequenceSetId()))
5320     {
5321       throw new Error(MessageManager.getString(
5322               "error.implementation_error_cannot_show_view_alignment_frame"));
5323     }
5324     if (tabbedPane != null && tabbedPane.getTabCount() > 0 && alignPanels
5325             .indexOf(alignmentPanel) != tabbedPane.getSelectedIndex())
5326     {
5327       tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5328     }
5329   }
5330
5331   /**
5332    * Action on selection of menu options to Show or Hide annotations.
5333    *
5334    * @param visible
5335    * @param forSequences
5336    *          update sequence-related annotations
5337    * @param forAlignment
5338    *          update non-sequence-related annotations
5339    */
5340   @Override
5341   protected void setAnnotationsVisibility(boolean visible,
5342           boolean forSequences, boolean forAlignment)
5343   {
5344     AlignmentAnnotation[] anns = alignPanel.getAlignment()
5345             .getAlignmentAnnotation();
5346     if (anns == null)
5347     {
5348       return;
5349     }
5350     for (AlignmentAnnotation aa : anns)
5351     {
5352       /*
5353        * don't display non-positional annotations on an alignment
5354        */
5355       if (aa.annotations == null)
5356       {
5357         continue;
5358       }
5359       boolean apply = (aa.sequenceRef == null && forAlignment)
5360               || (aa.sequenceRef != null && forSequences);
5361       if (apply)
5362       {
5363         aa.visible = visible;
5364       }
5365     }
5366     alignPanel.validateAnnotationDimensions(true);
5367     alignPanel.alignmentChanged();
5368   }
5369
5370   /**
5371    * Store selected annotation sort order for the view and repaint.
5372    */
5373   @Override
5374   protected void sortAnnotations_actionPerformed()
5375   {
5376     this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5377     this.alignPanel.av
5378             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5379     alignPanel.paintAlignment(false, false);
5380   }
5381
5382   /**
5383    *
5384    * @return alignment panels in this alignment frame
5385    */
5386   public List<? extends AlignmentViewPanel> getAlignPanels()
5387   {
5388     return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5389   }
5390
5391   /**
5392    * Open a new alignment window, with the cDNA associated with this (protein)
5393    * alignment, aligned as is the protein.
5394    */
5395   protected void viewAsCdna_actionPerformed()
5396   {
5397     // TODO no longer a menu action - refactor as required
5398     final AlignmentI alignment = getViewport().getAlignment();
5399     List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5400     if (mappings == null)
5401     {
5402       return;
5403     }
5404     List<SequenceI> cdnaSeqs = new ArrayList<>();
5405     for (SequenceI aaSeq : alignment.getSequences())
5406     {
5407       for (AlignedCodonFrame acf : mappings)
5408       {
5409         SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5410         if (dnaSeq != null)
5411         {
5412           /*
5413            * There is a cDNA mapping for this protein sequence - add to new
5414            * alignment. It will share the same dataset sequence as other mapped
5415            * cDNA (no new mappings need to be created).
5416            */
5417           final Sequence newSeq = new Sequence(dnaSeq);
5418           newSeq.setDatasetSequence(dnaSeq);
5419           cdnaSeqs.add(newSeq);
5420         }
5421       }
5422     }
5423     if (cdnaSeqs.size() == 0)
5424     {
5425       // show a warning dialog no mapped cDNA
5426       return;
5427     }
5428     AlignmentI cdna = new Alignment(
5429             cdnaSeqs.toArray(new SequenceI[cdnaSeqs.size()]));
5430     GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5431             AlignFrame.DEFAULT_HEIGHT);
5432     cdna.alignAs(alignment);
5433     String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5434             + this.title;
5435     Desktop.addInternalFrame(alignFrame, newtitle, AlignFrame.DEFAULT_WIDTH,
5436             AlignFrame.DEFAULT_HEIGHT);
5437   }
5438
5439   /**
5440    * Set visibility of dna/protein complement view (available when shown in a
5441    * split frame).
5442    *
5443    * @param show
5444    */
5445   @Override
5446   protected void showComplement_actionPerformed(boolean show)
5447   {
5448     SplitContainerI sf = getSplitViewContainer();
5449     if (sf != null)
5450     {
5451       sf.setComplementVisible(this, show);
5452     }
5453   }
5454
5455   /**
5456    * Generate the reverse (optionally complemented) of the selected sequences,
5457    * and add them to the alignment
5458    */
5459   @Override
5460   protected void showReverse_actionPerformed(boolean complement)
5461   {
5462     AlignmentI al = null;
5463     try
5464     {
5465       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5466       al = dna.reverseCdna(complement);
5467       viewport.addAlignment(al, "");
5468       addHistoryItem(new EditCommand(
5469               MessageManager.getString("label.add_sequences"), Action.PASTE,
5470               al.getSequencesArray(), 0, al.getWidth(),
5471               viewport.getAlignment()));
5472     } catch (Exception ex)
5473     {
5474       System.err.println(ex.getMessage());
5475       return;
5476     }
5477   }
5478
5479   /**
5480    * Try to run a script in the Groovy console, having first ensured that this
5481    * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5482    * be targeted at this alignment.
5483    */
5484   @Override
5485   protected void runGroovy_actionPerformed()
5486   {
5487     Jalview.setCurrentAlignFrame(this);
5488     groovy.ui.Console console = Desktop.getGroovyConsole();
5489     if (console != null)
5490     {
5491       try
5492       {
5493         console.runScript();
5494       } catch (Exception ex)
5495       {
5496         System.err.println((ex.toString()));
5497         JvOptionPane.showInternalMessageDialog(Desktop.desktop,
5498                 MessageManager.getString("label.couldnt_run_groovy_script"),
5499                 MessageManager.getString("label.groovy_support_failed"),
5500                 JvOptionPane.ERROR_MESSAGE);
5501       }
5502     }
5503     else
5504     {
5505       System.err.println("Can't run Groovy script as console not found");
5506     }
5507   }
5508
5509   /**
5510    * Hides columns containing (or not containing) a specified feature, provided
5511    * that would not leave all columns hidden
5512    *
5513    * @param featureType
5514    * @param columnsContaining
5515    * @return
5516    */
5517   public boolean hideFeatureColumns(String featureType,
5518           boolean columnsContaining)
5519   {
5520     boolean notForHiding = avc.markColumnsContainingFeatures(
5521             columnsContaining, false, false, featureType);
5522     if (notForHiding)
5523     {
5524       if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5525               false, featureType))
5526       {
5527         getViewport().hideSelectedColumns();
5528         return true;
5529       }
5530     }
5531     return false;
5532   }
5533
5534   @Override
5535   protected void selectHighlightedColumns_actionPerformed(
5536           ActionEvent actionEvent)
5537   {
5538     // include key modifier check in case user selects from menu
5539     avc.markHighlightedColumns(
5540             (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0, true,
5541             (actionEvent.getModifiers() & (ActionEvent.META_MASK
5542                     | ActionEvent.CTRL_MASK)) != 0);
5543   }
5544
5545   /**
5546    * Rebuilds the Colour menu, including any user-defined colours which have
5547    * been loaded either on startup or during the session
5548    */
5549   public void buildColourMenu()
5550   {
5551     colourMenu.removeAll();
5552
5553     colourMenu.add(applyToAllGroups);
5554     colourMenu.add(textColour);
5555     colourMenu.addSeparator();
5556
5557     ColourMenuHelper.addMenuItems(colourMenu, this, viewport.getAlignment(),
5558             false);
5559
5560     colourMenu.addSeparator();
5561     colourMenu.add(conservationMenuItem);
5562     colourMenu.add(modifyConservation);
5563     colourMenu.add(abovePIDThreshold);
5564     colourMenu.add(modifyPID);
5565     colourMenu.add(annotationColour);
5566
5567     ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
5568     ColourMenuHelper.setColourSelected(colourMenu, colourScheme);
5569   }
5570
5571   /**
5572    * Open a dialog (if not already open) that allows the user to select and
5573    * calculate PCA or Tree analysis
5574    */
5575   protected void openTreePcaDialog()
5576   {
5577     if (alignPanel.getCalculationDialog() == null)
5578     {
5579       new CalculationChooser(AlignFrame.this);
5580     }
5581   }
5582 }
5583
5584 class PrintThread extends Thread
5585 {
5586   AlignmentPanel ap;
5587
5588   public PrintThread(AlignmentPanel ap)
5589   {
5590     this.ap = ap;
5591   }
5592
5593   static PageFormat pf;
5594
5595   @Override
5596   public void run()
5597   {
5598     PrinterJob printJob = PrinterJob.getPrinterJob();
5599
5600     if (pf != null)
5601     {
5602       printJob.setPrintable(ap, pf);
5603     }
5604     else
5605     {
5606       printJob.setPrintable(ap);
5607     }
5608
5609     if (printJob.printDialog())
5610     {
5611       try
5612       {
5613         printJob.print();
5614       } catch (Exception PrintException)
5615       {
5616         PrintException.printStackTrace();
5617       }
5618     }
5619   }
5620 }